Re: [gmx-users] energy minimization
Gas phase simulations the inter-molecular interactions are smaller, and intra-molecular interactions dominate. Therefore total energy will be positive. If it was filled with a solvent i.e. liquid phase, then inter-molecular inteactions dominate and the total energy will be negative. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Tue, 14 Apr 2020 at 01:59, Afsane Farhadi wrote: > hi friends I generated a box of mixed gas with gmx insert-moleculesI > ran an energy minimizing. the potential energy is 4.05e+07 and maximum > force is 1.25e+03.I used different algorithm likes cg and steep for > minimization. what do I have to do untill my system potential energy has > negative value??I need a information about energy minimizing and potential > energy. I know that positive value of potential energy means the > intermolecular interaction is weaker than intramolecular interaction but I > don't know how I can control this matter. please help > > Sent from Yahoo Mail on Android > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing. the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative value??I need a information about energy minimizing and potential energy. I know that positive value of potential energy means the intermolecular interaction is weaker than intramolecular interaction but I don't know how I can control this matter. please help Sent from Yahoo Mail on Android -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization in vacuum
Hi, If u minimise the protein in vaccum...the bad contact within the protein atoms will be removed After solvation if u do...then both the bad water contact and steric clashes within the protein will be removed. On Mon 16 Mar, 2020, 8:37 PM Deepanshi ., wrote: > Dear all, > > I am trying to simulate an all atom protein in water. I wanted to ask that > what is the importance of minimizing the protein in a vacuum. It is not > mentioned in the lysozyme tutorial. > > Thanks. > > Regards, > Deepanshi > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization in vacuum
Dear all, I am trying to simulate an all atom protein in water. I wanted to ask that what is the importance of minimizing the protein in a vacuum. It is not mentioned in the lysozyme tutorial. Thanks. Regards, Deepanshi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization
This all sounds like http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc Remember, the box is just a visualisation of what the system looks like, and you can move that box anywhere. What is in the center of the box is entirely up to you and the post processing you do. What comes out of the mdrun engine is arbitrary. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 26 Feb 2020 at 08:13, Mohamed Abdelaal wrote: > Hello all, > > I created a graphene sheet and performed energy minimization, after energy > minimization I found that parts of the graphene sheet was moved from the > box bottom to the box topside at the same place (as if it was translated > upwards). I looked online for the problem and I understood that I should > restrain the graphene sheet along the z axis. I did that using force =1000. > and the problem was solved and nothing moved. > > After that I tried to insert 25 molecule of (C60) inside a box which > contains the graphene sheet. I did that and did the energy minimization but > part of the graphene sheet moved again from its place although the maximum > force was less than 1000 which is the force I used to restrain the graphene > sheet. However I didn't have any error during the energy minimization. Does > this means that the problem is just in visualization or I might have a > problem in my energy minimization ? > > It is also worth mentioning that the C60 molecules are not spherical as it > should be. I read about that and I found people mentioning that this shape > deformation in only a visualization problem and can be solved by using gmx > trjconv. is it possible that this problem has happened to my whole system > including the graphene sheet or it shouldn't affect my graphene sheet as > long as I have restrained it ? > > more info: > I used periodic_molecules = yes while trying to minimize my whole system. > (I also tried without it but no impact) > I wrote: > > gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p > C60_GRM_box.top -o min1.tpr -maxwarn 2 > > followed by > gmx mdrun -v -deffnm min1 > > and I got the below result: > writing lowest energy coordinates. > > Steepest Descents converged to Fmax < 1000 in 3293 steps > Potential Energy = 6.3598562e+05 > Maximum force = 9.9486487e+02 on atom 12087 > Norm of force = 6.5454323e+01 > > Can anybody help me please. > > Thanks > > Mohamed > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization
Hello all, I created a graphene sheet and performed energy minimization, after energy minimization I found that parts of the graphene sheet was moved from the box bottom to the box topside at the same place (as if it was translated upwards). I looked online for the problem and I understood that I should restrain the graphene sheet along the z axis. I did that using force =1000. and the problem was solved and nothing moved. After that I tried to insert 25 molecule of (C60) inside a box which contains the graphene sheet. I did that and did the energy minimization but part of the graphene sheet moved again from its place although the maximum force was less than 1000 which is the force I used to restrain the graphene sheet. However I didn't have any error during the energy minimization. Does this means that the problem is just in visualization or I might have a problem in my energy minimization ? It is also worth mentioning that the C60 molecules are not spherical as it should be. I read about that and I found people mentioning that this shape deformation in only a visualization problem and can be solved by using gmx trjconv. is it possible that this problem has happened to my whole system including the graphene sheet or it shouldn't affect my graphene sheet as long as I have restrained it ? more info: I used periodic_molecules = yes while trying to minimize my whole system. (I also tried without it but no impact) I wrote: gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p C60_GRM_box.top -o min1.tpr -maxwarn 2 followed by gmx mdrun -v -deffnm min1 and I got the below result: writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 3293 steps Potential Energy = 6.3598562e+05 Maximum force = 9.9486487e+02 on atom 12087 Norm of force = 6.5454323e+01 Can anybody help me please. Thanks Mohamed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization problem for POPE/POPG soluted bilayer taken from M. Karttunen website
Dear users I tried energy minimization of POPE/POPG bilayer from http://www.softsimu.net/downloads/pepg-mix.pdb . Process stopped and forces have not converged to requested precision (output shown below). I used Gromacs version 2019.2 . My colleague also used this bilayer before with earlier version of Gromacs (don't know which one, sorry, few years ago), and everything works fine. I tried a few different bilayers constructed from this one, and noticed that different atoms causes a problem (Fmax on it) but each time it's about H6 atom in some DPO molecule. I checked, and there is no steric clashes with periodic images or solution molecules. Any suggestions what could be wrong? Thanks Below are tipical gromacs output and mdp file: * Gromacs output: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step=0, Dmax= 1.0e-02 nm, Epot= -3.45240e+05 Fmax= 6.29238e+03, atom= 5580 Step=1, Dmax= 1.0e-02 nm, Epot= -3.51348e+05 Fmax= 3.62527e+03, atom= 1772 Step=2, Dmax= 1.2e-02 nm, Epot= -3.55043e+05 Fmax= 1.07906e+04, atom= 1772 Step=3, Dmax= 1.4e-02 nm, Epot= -3.58399e+05 Fmax= 6.04668e+03, atom= 524 Step=4, Dmax= 1.7e-02 nm, Epot= -3.58764e+05 Fmax= 1.66084e+04, atom= 524 Step=5, Dmax= 2.1e-02 nm, Epot= -3.62991e+05 Fmax= 3.55133e+04, atom= 6325 Step=6, Dmax= 2.5e-02 nm, Epot= -3.66326e+05 Fmax= 3.14946e+05, atom= 6325 Step=7, Dmax= 3.0e-02 nm, Epot= -3.66358e+05 Fmax= 6.27472e+04, atom= 6005 Step=8, Dmax= 3.6e-02 nm, Epot= -3.70907e+05 Fmax= 7.76457e+05, atom= 6217 Step= 10, Dmax= 2.1e-02 nm, Epot= -3.71321e+05 Fmax= 1.24828e+06, atom= 5581 Step= 14, Dmax= 3.2e-03 nm, Epot= -4.38973e+05 Fmax= 7.26301e+07, atom= 5583 Step= 18, Dmax= 4.8e-04 nm, Epot= -4.39005e+05 Fmax= 1.17286e+08, atom= 5581 Step= 28, Dmax= 1.1e-06 nm, Epot= -4.39005e+05 Fmax= 1.16818e+08, atom= 5581 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. *** minim.mdp: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5 nstlist = 1; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME rcoulomb = 1.2 rvdw = 1.2 pbc= xyz * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Hi, Typical force fields will have negative energies at minimize configurations, but my guess is that your initial configuration has some serious problem. Did you visualise the minimization start and end points? Mark On Tue., 27 Aug. 2019, 18:52 Dhrubajyoti Maji, wrote: > Dear gromacs users, > I am doing energy minimization of a neat urea system. When I set emtol = > 10 the following result is obtained : > Steepest Descents converged to machine precision in 33995 steps, > but did not reach the requested Fmax < 10. > Potential Energy = 6.7910172e+04 > Maximum force = 7.8070724e+01 on atom 353 > Norm of force = 3.1714432e+00 > and average energy is > Energy Average Err.Est. RMSD Tot-Drift > > --- > Potential 72421.6 250014229.1 -16147.4 > (kJ/mol) > And when I set emtol=100 the following result is obtained : > Steepest Descents converged to Fmax < 100 in 12573 steps > Potential Energy = 7.1502609e+04 > Maximum force = 8.5925835e+01 on atom 2713 > Norm of force = 5.0333209e+00 > and average energy is > Energy Average Err.Est. RMSD Tot-Drift > > --- > Potential 77654.4 360022408.3 -22901.6 > (kJ/mol) > In both cases the energy is well converged but not less than zero. Does > only convergence of potential energy (not negative) guarantee the > completion of EM process ? If so then what emtol value should I use ? > Any help will be highly appreciated. Thanks for your time. > Best regards > Dhrubajyoti Maji > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Dear gromacs users, I am doing energy minimization of a neat urea system. When I set emtol = 10 the following result is obtained : Steepest Descents converged to machine precision in 33995 steps, but did not reach the requested Fmax < 10. Potential Energy = 6.7910172e+04 Maximum force = 7.8070724e+01 on atom 353 Norm of force = 3.1714432e+00 and average energy is Energy Average Err.Est. RMSD Tot-Drift --- Potential 72421.6 250014229.1 -16147.4 (kJ/mol) And when I set emtol=100 the following result is obtained : Steepest Descents converged to Fmax < 100 in 12573 steps Potential Energy = 7.1502609e+04 Maximum force = 8.5925835e+01 on atom 2713 Norm of force = 5.0333209e+00 and average energy is Energy Average Err.Est. RMSD Tot-Drift --- Potential 77654.4 360022408.3 -22901.6 (kJ/mol) In both cases the energy is well converged but not less than zero. Does only convergence of potential energy (not negative) guarantee the completion of EM process ? If so then what emtol value should I use ? Any help will be highly appreciated. Thanks for your time. Best regards Dhrubajyoti Maji -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Look around atom 2016, there is a bad contact between the atoms in that area, hence the infinite force, very high potential energy, and the minimisation fails. On Tue, 25 Sep. 2018, 6:48 pm ikjk, <1761440...@qq.com> wrote: > hello >I am doing a md with martini force filed,I create a box, there is a > double monolayer, then I solvate it, but when I did energy minimization, > > gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then > > NOTE 1 [file minim.mdp]: > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note > that with the Verlet scheme, nstlist has no effect on the accuracy of > your simulation. > > Setting the LD random seed to 562058480 > Generated 0 of the 780 non-bonded parameter combinations > Excluding 1 bonded neighbours molecule type 'DPPC' > Excluding 1 bonded neighbours molecule type 'W' > Removing all charge groups because cutoff-scheme=Verlet > Analysing residue names: > There are: 72143 Other residues > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > Number of degrees of freedom in T-Coupling group rest is 261042.00 > Calculating fourier grid dimensions for X Y Z > Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118 > Estimate for the relative computational > load of the PME mesh part: 0.91 > > NOTE 2 [file minim.mdp]: > The optimal PME mesh load for parallel simulations is below 0.5 > and for highly parallel simulations between 0.25 and 0.33, > for higher performance, increase the cut-off and the PME grid spacing. > > > > > > > > > gmx mdrun -v -deffnm em > > > > Steepest Descents: >Tolerance (Fmax) = 1.0e+03 >Number of steps=5 > Step= 14, Dmax= 1.2e-06 nm, Epot= 2.36880e+22 Fmax= inf, atom= > 2016 > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your > system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > > writing lowest energy coordinates. > it just stopped with 14 steps, here is my mdp file,if you can solve this > problem, I will appreciate that. > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Minimization step size > nsteps = 5 ; Maximum number of (minimization) steps to > perform > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and > long range forces > cutoff-scheme = Verlet; Buffered neighbor searching > ns_type = grid ; Method to determine neighbor list (simple, > grid) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb= 1.0 ; Short-range electrostatic cut-off > rvdw= 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions in all 3 > dimensions > > > > > > > > > jiao > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
hello I am doing a md with martini force filed,I create a box, there is a double monolayer, then I solvate it, but when I did energy minimization, gmx grompp -f minim.mdp -c solv.gro -p dppc.top -o em.tpr then NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 562058480 Generated 0 of the 780 non-bonded parameter combinations Excluding 1 bonded neighbours molecule type 'DPPC' Excluding 1 bonded neighbours molecule type 'W' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 72143 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 261042.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 168x168x208, spacing 0.118 0.118 0.118 Estimate for the relative computational load of the PME mesh part: 0.91 NOTE 2 [file minim.mdp]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing. gmx mdrun -v -deffnm em Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.36880e+22 Fmax= inf, atom= 2016 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. writing lowest energy coordinates. it just stopped with 14 steps, here is my mdp file,if you can solve this problem, I will appreciate that. ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions jiao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
LigParGen generates new atom types for each ligand topology it generates. The output files from LigParGen should contain terms for opls800-925 (if necessary) in the generated topology file. These need to be included in the force-field file you use for use in your simulations. A warning should be made about LigParGen: each atom is given a unique atomtype. For instance if you have a 25 atom ligand, you will have atomtypes opls 800 through opls824. Some of these may be repeats. This means that if you want to run with a different ligand you have to change these atomtype definitions each time. Hope that helps. === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Wednesday, July 25, 2018 8:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization On 7/24/18 7:24 AM, farial tavakoli wrote: > Dear Justin > > I used LigParGen server to generate ligand topology but I dont know what > changes I have to do in .itp file. > when I issued this command: > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor > > faced this error:ERROR 1 [file LIG.itp, line 11]: >Atomtype opls_800 not found > I checked the aminoacids.rtp file of > /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not > atomtype opls_800 and 801 and ... in this file. while the LIG.itp which > generated by LigParGen server has atomtype opls_800 , 801 and ... . > I have to modify all of these atomtype opls_ in order to correspond to with > aminoacid.rtp file? > I would be thankfull if you help me. > bestFraial It looks like your topology introduces new atom types. Check the LigParGen documentation to see if it requires a different version of the force field or if the parameters are provided somewhere. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 7/24/18 7:24 AM, farial tavakoli wrote: Dear Justin I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. when I issued this command: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor faced this error:ERROR 1 [file LIG.itp, line 11]: Atomtype opls_800 not found I checked the aminoacids.rtp file of /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype opls_800 and 801 and ... in this file. while the LIG.itp which generated by LigParGen server has atomtype opls_800 , 801 and ... . I have to modify all of these atomtype opls_ in order to correspond to with aminoacid.rtp file? I would be thankfull if you help me. bestFraial It looks like your topology introduces new atom types. Check the LigParGen documentation to see if it requires a different version of the force field or if the parameters are provided somewhere. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Dear Justin I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. when I issued this command: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor faced this error:ERROR 1 [file LIG.itp, line 11]: Atomtype opls_800 not found I checked the aminoacids.rtp file of /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype opls_800 and 801 and ... in this file. while the LIG.itp which generated by LigParGen server has atomtype opls_800 , 801 and ... . I have to modify all of these atomtype opls_ in order to correspond to with aminoacid.rtp file? I would be thankfull if you help me. bestFraial On Monday, July 16, 2018, 5:29:17 PM GMT+4:30, Justin Lemkul wrote: On 7/16/18 3:49 AM, farial tavakoli wrote: > Dear Justin > > Thank you for your reply > I noticed my problem ( the reason was topolgen.pl name in my directory, it is > named topologen_1.1.pl in the working directory) > I generated my ligand topology but got this : > No output type specified. Using default type of .top > Unknown atom type: N 13 with 2 bonds - cannot assign atom type. > Using default H type for atom 16. > Using default H type for atom 26. > Using default H type for atom 31. > Using default H type for atom 38. > Using default H type for atom 39. > Using default H type for atom 40. > Using default H type for atom 41. > Unknown atom type: N 42 with 2 bonds - cannot assign atom type. > Using default H type for atom 47. > Using default H type for atom 48. > Using default H type for atom 49. > Using default H type for atom 50. > Using default H type for atom 51. > Using default H type for atom 52. > > > WARNING: Net charge on the molecule is -2.781 > You will need to make corrections to the output topology > > > TopolGen, version 1.1_dev (10/14/2009) complete. > > Output topology has been written. An attempt has been made to assign charges > and atom types based > on existing functional groups, but they may not be correct. No charge > calculations or other > parameterization calculations have been done. Guesses have been made for > charge groups. Please > inspect and correct the topology before using it in any simulations. The > author of the script does > NOT guarantee accuracy or usability of any of the content; TopolGen was > written as a convenience > for outputting a skeleton topology, and nothing more. Heed the above warning. TopolGen assigns parameters based on similarity to known functional groups. If your molecule has something unusual, it makes no attempt to try to assign reasonable parameters. You'll need to actually parametrize the molecule. Make use of available web servers like LikeParGen or others. -Justin > > the N13 atom connected to C with double bond. it sounds topolgen can not > identify N atom in 2 bonds with C . > would you please help me to figure out this problem > thans in advanceFarial > > On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul > wrote: > > > > On 7/15/18 1:38 AM, farial tavakoli wrote: >> Dear Justin >> >> But I copied & pasted topolgen and perl5 folders in the working directory. >> and faced the mentioned error. >> >> Can't open perl script "topolgen.pl": No such file or directory >> I dont know how I should figure out this problem. > The problem is still the same: there's nothing called "topolgen.pl" in > the working directory. List your files, you'll see it's called something > else. > >> Which one of all-atom force fields will you choose to run a simulation on a >> complex with small molecule, if you want to calculate binding energy using >> G_MMPBSA ?I really need your guidance . > Presumably any of them, but I don't do such calculations. > > -Justin > -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 7/16/18 3:49 AM, farial tavakoli wrote: Dear Justin Thank you for your reply I noticed my problem ( the reason was topolgen.pl name in my directory, it is named topologen_1.1.pl in the working directory) I generated my ligand topology but got this : No output type specified. Using default type of .top Unknown atom type: N 13 with 2 bonds - cannot assign atom type. Using default H type for atom 16. Using default H type for atom 26. Using default H type for atom 31. Using default H type for atom 38. Using default H type for atom 39. Using default H type for atom 40. Using default H type for atom 41. Unknown atom type: N 42 with 2 bonds - cannot assign atom type. Using default H type for atom 47. Using default H type for atom 48. Using default H type for atom 49. Using default H type for atom 50. Using default H type for atom 51. Using default H type for atom 52. WARNING: Net charge on the molecule is -2.781 You will need to make corrections to the output topology TopolGen, version 1.1_dev (10/14/2009) complete. Output topology has been written. An attempt has been made to assign charges and atom types based on existing functional groups, but they may not be correct. No charge calculations or other parameterization calculations have been done. Guesses have been made for charge groups. Please inspect and correct the topology before using it in any simulations. The author of the script does NOT guarantee accuracy or usability of any of the content; TopolGen was written as a convenience for outputting a skeleton topology, and nothing more. Heed the above warning. TopolGen assigns parameters based on similarity to known functional groups. If your molecule has something unusual, it makes no attempt to try to assign reasonable parameters. You'll need to actually parametrize the molecule. Make use of available web servers like LikeParGen or others. -Justin the N13 atom connected to C with double bond. it sounds topolgen can not identify N atom in 2 bonds with C . would you please help me to figure out this problem thans in advanceFarial On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul wrote: On 7/15/18 1:38 AM, farial tavakoli wrote: Dear Justin But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error. Can't open perl script "topolgen.pl": No such file or directory I dont know how I should figure out this problem. The problem is still the same: there's nothing called "topolgen.pl" in the working directory. List your files, you'll see it's called something else. Which one of all-atom force fields will you choose to run a simulation on a complex with small molecule, if you want to calculate binding energy using G_MMPBSA ?I really need your guidance . Presumably any of them, but I don't do such calculations. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Dear Justin Thank you for your reply I noticed my problem ( the reason was topolgen.pl name in my directory, it is named topologen_1.1.pl in the working directory) I generated my ligand topology but got this : No output type specified. Using default type of .top Unknown atom type: N 13 with 2 bonds - cannot assign atom type. Using default H type for atom 16. Using default H type for atom 26. Using default H type for atom 31. Using default H type for atom 38. Using default H type for atom 39. Using default H type for atom 40. Using default H type for atom 41. Unknown atom type: N 42 with 2 bonds - cannot assign atom type. Using default H type for atom 47. Using default H type for atom 48. Using default H type for atom 49. Using default H type for atom 50. Using default H type for atom 51. Using default H type for atom 52. WARNING: Net charge on the molecule is -2.781 You will need to make corrections to the output topology TopolGen, version 1.1_dev (10/14/2009) complete. Output topology has been written. An attempt has been made to assign charges and atom types based on existing functional groups, but they may not be correct. No charge calculations or other parameterization calculations have been done. Guesses have been made for charge groups. Please inspect and correct the topology before using it in any simulations. The author of the script does NOT guarantee accuracy or usability of any of the content; TopolGen was written as a convenience for outputting a skeleton topology, and nothing more. the N13 atom connected to C with double bond. it sounds topolgen can not identify N atom in 2 bonds with C . would you please help me to figure out this problem thans in advanceFarial On Sunday, July 15, 2018, 5:23:41 PM GMT+4:30, Justin Lemkul wrote: On 7/15/18 1:38 AM, farial tavakoli wrote: > Dear Justin > > But I copied & pasted topolgen and perl5 folders in the working directory. > and faced the mentioned error. > > Can't open perl script "topolgen.pl": No such file or directory > I dont know how I should figure out this problem. The problem is still the same: there's nothing called "topolgen.pl" in the working directory. List your files, you'll see it's called something else. > Which one of all-atom force fields will you choose to run a simulation on a > complex with small molecule, if you want to calculate binding energy using > G_MMPBSA ?I really need your guidance . Presumably any of them, but I don't do such calculations. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 7/15/18 1:38 AM, farial tavakoli wrote: Dear Justin But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error. Can't open perl script "topolgen.pl": No such file or directory I dont know how I should figure out this problem. The problem is still the same: there's nothing called "topolgen.pl" in the working directory. List your files, you'll see it's called something else. Which one of all-atom force fields will you choose to run a simulation on a complex with small molecule, if you want to calculate binding energy using G_MMPBSA ?I really need your guidance . Presumably any of them, but I don't do such calculations. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Dear Justin But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error. Can't open perl script "topolgen.pl": No such file or directory I dont know how I should figure out this problem. Which one of all-atom force fields will you choose to run a simulation on a complex with small molecule, if you want to calculate binding energy using G_MMPBSA ?I really need your guidance . best Farial On Saturday, July 14, 2018, 6:35:27 PM GMT+4:30, Justin Lemkul wrote: On 7/14/18 5:03 AM, farial tavakoli wrote: > > Dear justin > > I am trying to run a simulation on my complex which has small molecule as a > ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then > installed perl script on linux. then typed "perl -v" to check if it is > installed. the perl 5.20.1 was installed. > but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type > itp/top] " command to generate ligand topology , faced with this error: > Can't open perl script "topolgen.pl": No such file or directory > Infact I am new user in generation topology for small molecules using OPLSAA > ff. Would you please help me to figure out this problem? "No such file or directory" means the file isn't in the working directory. This is a generic error message from your shell and nothing specific about the script itself. -Justin > > Farial > best > On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul > wrote: > > > > On 2/20/18 12:52 PM, farial tavakoli wrote: >> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px >>#715FFA solid !important; padding-left:1ex !important; background-color:white >>!important; } Dear Justin >> Thank you for the reply >> You meant , to tweak the emtol doesn't have noticable affects on the >> conformational enssemble generated by MD? >> > Precisely what I said, yes. > > -Justin > >> Sent from Yahoo Mail for iPhone >> >> >> On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul >> wrote: >> >> >> >> On 2/20/18 4:52 AM, farial tavakoli wrote: >>> Dear GMX users >>> I used CHARMM36 all atom force field to generate .top and .gro files for my >>> complex composed of a receptor protein and a ligand with 2 phosphotyrosine >>> residues, then ran a md simulation on it and then used g_mmpbsa to >>> calculate the binding free energy by pdies ( 2 and 4) but got + 426 and >>> +527 kjol/mol, respectively. While, I calculated binding energy before for >>> many other complexes without any phosphate groups using OPLS all atom force >>> field and pdie = 2 and obtained minus energy. But this time , I dont know >>> why I got positive binding energy? Is it because of charmm36 all atom force >>> field , the phosphate groups or it is needed to be energy minimized under >>> more restriction situations? >>> I am checking different factors to understand its reason, so I wanted to >>> know , would it be ok if I energy minimize the complex with more >>> restriction situations ? for example by specifying emtol under 1000 >>> kj/mol/nm , like 800 ? I think the positive binding energy might be because >>> of the complex didnt minimized well. however I checked the em.log file and >>> saw it was minimized well: >>> >>> Steepest Descents converged to Fmax < 1000 in 241 steps >>> Potential Energy = -6.5047744e+05 >>> Maximum force = 9.8285083e+02 on atom 3335 >>> Norm of force = 3.6905827e+01 >>> Is there anyone can advice me in energy minimization with emtol 800? >> The purpose of energy minimization is to establish a reasonable starting >> point for your simulation. Tweaks to emtol will have little to no >> noticeable bearing on the conformational ensemble generated by MD. >> >> -Justin >> -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 7/14/18 5:03 AM, farial tavakoli wrote: Dear justin I am trying to run a simulation on my complex which has small molecule as a ligand , using OPLSAA ff. so I downloaded the topolgen-1.1.tgz and then installed perl script on linux. then typed "perl -v" to check if it is installed. the perl 5.20.1 was installed. but when I typed " perl topolgen.pl -f input.pdb -o output.top [-type itp/top] " command to generate ligand topology , faced with this error: Can't open perl script "topolgen.pl": No such file or directory Infact I am new user in generation topology for small molecules using OPLSAA ff. Would you please help me to figure out this problem? "No such file or directory" means the file isn't in the working directory. This is a generic error message from your shell and nothing specific about the script itself. -Justin Farial best On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkul wrote: On 2/20/18 12:52 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have noticable affects on the conformational enssemble generated by MD? Precisely what I said, yes. -Justin Sent from Yahoo Mail for iPhone On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul wrote: On 2/20/18 4:52 AM, farial tavakoli wrote: Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations? I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well: Steepest Descents converged to Fmax < 1000 in 241 steps Potential Energy = -6.5047744e+05 Maximum force = 9.8285083e+02 on atom 3335 Norm of force = 3.6905827e+01 Is there anyone can advice me in energy minimization with emtol 800? The purpose of energy minimization is to establish a reasonable starting point for your simulation. Tweaks to emtol will have little to no noticeable bearing on the conformational ensemble generated by MD. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization of solvated MOFs.
Have you visualised the system to see what it is about that water that is generating such a high force? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Wed, 11 Jul 2018 at 00:57, Nagasree Garapati wrote: > > > Hi > > > I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I > have obtained both structure file (from CCDC) and forcefield data from > literature and I was able to successfully run energy minimization, and > equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But > when I tried to perform energy minimization for a system of MOF in water (by > putting MOF in a box and solvating using gmx solvate), I am getting following > message and forces are very high on water molecules. I am not how to overcome > this problem, any thoughts are appreciated. > > > "Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 5 (which may not be possible for your system). It > stopped because the algorithm tried to make a new step whose size was too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 95 steps, > but did not reach the requested Fmax < 5. > Potential Energy = -3.38556029741624e+13 > Maximum force = 2.45386477264935e+25 on atom 306 > Norm of force = 1.49337454338593e+24" > > > > Thank You > > > > With Regards > Nagasree Garapati > Research Assistant Professor > Dept of Chemical and Biomedical Engineering > West Virginia University > PO Box 6102 > Morgantown, WV 26506-6102 > 304 293-5028(O) > 304 276-3674(M) > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization of solvated MOFs.
Hi I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I have obtained both structure file (from CCDC) and forcefield data from literature and I was able to successfully run energy minimization, and equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But when I tried to perform energy minimization for a system of MOF in water (by putting MOF in a box and solvating using gmx solvate), I am getting following message and forces are very high on water molecules. I am not how to overcome this problem, any thoughts are appreciated. "Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 5 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. writing lowest energy coordinates. Steepest Descents converged to machine precision in 95 steps, but did not reach the requested Fmax < 5. Potential Energy = -3.38556029741624e+13 Maximum force = 2.45386477264935e+25 on atom 306 Norm of force = 1.49337454338593e+24" Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization with Walls
Hello, I am trying to put together a mdp script for energy minimization using 2 walls in the z direction. I have a slab of just water which is simulated fine if i remove the walls section from the script. when I add the wall section, I start to receive this error "Fatal error: DD cell 4 4 0 could only obtain 19 of the 20 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; My script ; LINES STARTING WITH ';' ARE COMMENTS ;title = Minimization ; Title of run define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force < 1.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform energygrps = system; Which energy group(s) to write to disk nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 pbc = xy; pbc in xy only nwall = 2 ; wall at z=0 and z=z-box wall-type = 10-4 ; direct 12-6 LJ as fn of distance from wall wall-density= 20 20 wall-atomtype = CA CA wall-r-linpot = 1 ewald-geometry = 3dc ; Only Ewald sum compatible with slab geometry, requires box_height >= slab_height * 3 wall-ewald-zfac = 3 ; Extra empty space for slab geometry calculation (reducing coulomb interaction) I hope someone could help me figure what is the problem Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Dear Justin In according to obtaining positive binding free energy using g_mmpbsa for my complex which has 2 phosphotyrosine residues and is simulated by charmm36 force field , I sent an email to g_mmpbsa mailing list and informed them to help me for solving my problem, but they replied me : " we have not tested the g_mmpbsa with charmm36 so we can't say about the validity. Other members of g_mmpbsa tool, also previously reported about the positive binding energy when using charmm36 force field." I sent another email to them :would you please advice me how could I calculate the free binding energy of my complex (receptor and ligand that has 2 phosphotyrosine residues ) which has been simulated by charmm36 all atom force field? but I have not any response yet. so I decided to use a modified amber99s force field to use in gromacs to simulate my complex. and then use g_mmpbsa to calculate the binding energy. I searched the net and found this one to modify the amber99s ff : http://www.pharmacy.manchester.ac.uk/bryce/amberbut it is not for gromacs. Would you please advice me how can I get a modified amber force field to simulate my complex using gromacs?or help me how can I calcualte the binding energy of my complex which is simulated by charmm36 in gromacs? with best regardsFarial On Tuesday, February 20, 2018, 10:24:49 PM GMT+3:30, Justin Lemkulwrote: On 2/20/18 12:52 PM, farial tavakoli wrote: > blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px >#715FFA solid !important; padding-left:1ex !important; background-color:white >!important; } Dear Justin > Thank you for the reply > You meant , to tweak the emtol doesn't have noticable affects on the > conformational enssemble generated by MD? > Precisely what I said, yes. -Justin > > Sent from Yahoo Mail for iPhone > > > On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkul wrote: > > > > On 2/20/18 4:52 AM, farial tavakoli wrote: >> Dear GMX users >> I used CHARMM36 all atom force field to generate .top and .gro files for my >> complex composed of a receptor protein and a ligand with 2 phosphotyrosine >> residues, then ran a md simulation on it and then used g_mmpbsa to calculate >> the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, >> respectively. While, I calculated binding energy before for many other >> complexes without any phosphate groups using OPLS all atom force field and >> pdie = 2 and obtained minus energy. But this time , I dont know why I got >> positive binding energy? Is it because of charmm36 all atom force field , >> the phosphate groups or it is needed to be energy minimized under more >> restriction situations? >> I am checking different factors to understand its reason, so I wanted to >> know , would it be ok if I energy minimize the complex with more restriction >> situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 >> ? I think the positive binding energy might be because of the complex didnt >> minimized well. however I checked the em.log file and saw it was minimized >> well: >> >> Steepest Descents converged to Fmax < 1000 in 241 steps >> Potential Energy = -6.5047744e+05 >> Maximum force = 9.8285083e+02 on atom 3335 >> Norm of force = 3.6905827e+01 >> Is there anyone can advice me in energy minimization with emtol 800? > The purpose of energy minimization is to establish a reasonable starting > point for your simulation. Tweaks to emtol will have little to no > noticeable bearing on the conformational ensemble generated by MD. > > -Justin > -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 2/20/18 12:52 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have noticable affects on the conformational enssemble generated by MD? Precisely what I said, yes. -Justin Sent from Yahoo Mail for iPhone On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkulwrote: On 2/20/18 4:52 AM, farial tavakoli wrote: Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations? I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well: Steepest Descents converged to Fmax < 1000 in 241 steps Potential Energy = -6.5047744e+05 Maximum force = 9.8285083e+02 on atom 3335 Norm of force = 3.6905827e+01 Is there anyone can advice me in energy minimization with emtol 800? The purpose of energy minimization is to establish a reasonable starting point for your simulation. Tweaks to emtol will have little to no noticeable bearing on the conformational ensemble generated by MD. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear Justin Thank you for the reply You meant , to tweak the emtol doesn't have noticable affects on the conformational enssemble generated by MD? Sent from Yahoo Mail for iPhone On Tuesday, February 20, 2018, 9:03 PM, Justin Lemkulwrote: On 2/20/18 4:52 AM, farial tavakoli wrote: > Dear GMX users > I used CHARMM36 all atom force field to generate .top and .gro files for my > complex composed of a receptor protein and a ligand with 2 phosphotyrosine > residues, then ran a md simulation on it and then used g_mmpbsa to calculate > the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, > respectively. While, I calculated binding energy before for many other > complexes without any phosphate groups using OPLS all atom force field and > pdie = 2 and obtained minus energy. But this time , I dont know why I got > positive binding energy? Is it because of charmm36 all atom force field , the > phosphate groups or it is needed to be energy minimized under more > restriction situations? > I am checking different factors to understand its reason, so I wanted to know > , would it be ok if I energy minimize the complex with more restriction > situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 > ? I think the positive binding energy might be because of the complex didnt > minimized well. however I checked the em.log file and saw it was minimized > well: > > Steepest Descents converged to Fmax < 1000 in 241 steps > Potential Energy = -6.5047744e+05 > Maximum force = 9.8285083e+02 on atom 3335 > Norm of force = 3.6905827e+01 > Is there anyone can advice me in energy minimization with emtol 800? The purpose of energy minimization is to establish a reasonable starting point for your simulation. Tweaks to emtol will have little to no noticeable bearing on the conformational ensemble generated by MD. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On 2/20/18 4:52 AM, farial tavakoli wrote: Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations? I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well: Steepest Descents converged to Fmax < 1000 in 241 steps Potential Energy = -6.5047744e+05 Maximum force = 9.8285083e+02 on atom 3335 Norm of force = 3.6905827e+01 Is there anyone can advice me in energy minimization with emtol 800? The purpose of energy minimization is to establish a reasonable starting point for your simulation. Tweaks to emtol will have little to no noticeable bearing on the conformational ensemble generated by MD. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Dear GMX users I used CHARMM36 all atom force field to generate .top and .gro files for my complex composed of a receptor protein and a ligand with 2 phosphotyrosine residues, then ran a md simulation on it and then used g_mmpbsa to calculate the binding free energy by pdies ( 2 and 4) but got + 426 and +527 kjol/mol, respectively. While, I calculated binding energy before for many other complexes without any phosphate groups using OPLS all atom force field and pdie = 2 and obtained minus energy. But this time , I dont know why I got positive binding energy? Is it because of charmm36 all atom force field , the phosphate groups or it is needed to be energy minimized under more restriction situations? I am checking different factors to understand its reason, so I wanted to know , would it be ok if I energy minimize the complex with more restriction situations ? for example by specifying emtol under 1000 kj/mol/nm , like 800 ? I think the positive binding energy might be because of the complex didnt minimized well. however I checked the em.log file and saw it was minimized well: Steepest Descents converged to Fmax < 1000 in 241 steps Potential Energy = -6.5047744e+05 Maximum force = 9.8285083e+02 on atom 3335 Norm of force = 3.6905827e+01 Is there anyone can advice me in energy minimization with emtol 800? Thank in advanceFarial -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkulwrote: > > > On 1/6/18 10:10 AM, rose rahmani wrote: > >> Hi, >> >> I want to calculate the number of density profile of water.the initial >> .gro >> file which i have,has amino acid in itself, which should not be present in >> this analyze. So, i had to remove amino acid, and then, when i wanted to >> do >> energy minimization again, it's crushed and gave me step files. >> maybe it's because of modifying the initial gro file but i didn't have any >> choice i think so! because i have another structures in initial.gro file >> which i don't want to modify their coordinates.and all structure are in >> the >> center of box and the rest of the box should be empty. >> would you please help me? what is the alternative? >> > > Why do you have to remove the amino acid to do this analysis? I should study different amino acids one by one in my system.In literature there is just one NUMBER density profile scheme reported for all different( in amino acids) tests. This means that this profile should not depend on amino acids and should be token before amino acid is in. it's rational because as you said amino acid can change the distribution of water also its number density so different amino acids cause different changes, am i wrong? However in literature a few distance above surface is considered (1nm) and my amino acids are in about 1.7 far from surface ( because i want to do pulling in next step)but i think it's better to remove it( as i have not access to file before amino acid is in so i thought maybe it's better to remove it and do EM and equilibration again). What do you think,sir? BTW, how can i specify the gmx density to just calculate the specific distance above surface not whole box (Z dimension) ? Thank you > You're creating a rather large void, which will make nearby waters > unstable. In the analysis, you're going to have a volume occupied by the > amino acid that yields zero water density. That's going to happen > irrespective of whether or not you remove the amino acid, so save yourself > some trouble and don't mess with the coordinates. > > -Justin > > > with regards >> >> >> >> >> this is em.job >> >> Steepest Descents: >> Tolerance (Fmax) = 1.0e+01 >> Number of steps= 5000 >> Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom= >> 815 >> Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom= >> 4307 >> Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom= >> 4307 >> Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom= >> 4302 >> Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom= >> 4303 >> Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom= >> 4303 >> Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom= >> 4303 >> Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom= >> 4303 >> Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom= >> 4303 >> Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom= >> 4303 >> Step= 10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom= >> 4302 >> Step= 11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom= >> 4302 >> Step= 12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom= >> 4301 >> Step= 13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom= >> 4303 >> >> step 14: Water molecule starting at atom 2018 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> step 14: Water molecule starting at atom 1265 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> Wrote pdb files with previous and current coordinates >> Wrote pdb files with previous and current coordinates >> Step= 14, Dmax= 1.1e-01 nm, Epot= 2.77257e+05 Fmax= 2.29207e+09, atom= >> 2018^M >> step 15: Water molecule starting at atom 1331 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> Wrote pdb files with previous and current coordinates >> Step= 15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom= >> 1331^MStep= 16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02, >> atom= 4301 >> Step= 17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom= >> 4303 >> Step= 18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom= >> 4301 >> Step= 19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom= >> 4301 >> Step= 20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom= >> 4301 >> Step= 21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom= >> 4301 >> >> 140,1 >> . >> . >> . >> . >> > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of
Re: [gmx-users] energy minimization
On 1/6/18 10:10 AM, rose rahmani wrote: Hi, I want to calculate the number of density profile of water.the initial .gro file which i have,has amino acid in itself, which should not be present in this analyze. So, i had to remove amino acid, and then, when i wanted to do energy minimization again, it's crushed and gave me step files. maybe it's because of modifying the initial gro file but i didn't have any choice i think so! because i have another structures in initial.gro file which i don't want to modify their coordinates.and all structure are in the center of box and the rest of the box should be empty. would you please help me? what is the alternative? Why do you have to remove the amino acid to do this analysis? You're creating a rather large void, which will make nearby waters unstable. In the analysis, you're going to have a volume occupied by the amino acid that yields zero water density. That's going to happen irrespective of whether or not you remove the amino acid, so save yourself some trouble and don't mess with the coordinates. -Justin with regards this is em.job Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 5000 Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom= 815 Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom= 4307 Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom= 4307 Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom= 4302 Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom= 4303 Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom= 4303 Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom= 4303 Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom= 4303 Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom= 4303 Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom= 4303 Step= 10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom= 4302 Step= 11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom= 4302 Step= 12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom= 4301 Step= 13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom= 4303 step 14: Water molecule starting at atom 2018 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 14: Water molecule starting at atom 1265 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step= 14, Dmax= 1.1e-01 nm, Epot= 2.77257e+05 Fmax= 2.29207e+09, atom= 2018^M step 15: Water molecule starting at atom 1331 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom= 1331^MStep= 16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02, atom= 4301 Step= 17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom= 4303 Step= 18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom= 4301 Step= 19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom= 4301 Step= 20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom= 4301 Step= 21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom= 4301 140,1 . . . . -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi, I want to calculate the number of density profile of water.the initial .gro file which i have,has amino acid in itself, which should not be present in this analyze. So, i had to remove amino acid, and then, when i wanted to do energy minimization again, it's crushed and gave me step files. maybe it's because of modifying the initial gro file but i didn't have any choice i think so! because i have another structures in initial.gro file which i don't want to modify their coordinates.and all structure are in the center of box and the rest of the box should be empty. would you please help me? what is the alternative? with regards this is em.job Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 5000 Step=0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom= 815 Step=1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom= 4307 Step=2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom= 4307 Step=3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom= 4302 Step=4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom= 4303 Step=5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom= 4303 Step=6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom= 4303 Step=7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom= 4303 Step=8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom= 4303 Step=9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom= 4303 Step= 10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom= 4302 Step= 11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom= 4302 Step= 12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom= 4301 Step= 13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom= 4303 step 14: Water molecule starting at atom 2018 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. step 14: Water molecule starting at atom 1265 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Step= 14, Dmax= 1.1e-01 nm, Epot= 2.77257e+05 Fmax= 2.29207e+09, atom= 2018^M step 15: Water molecule starting at atom 1331 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Step= 15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom= 1331^MStep= 16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02, atom= 4301 Step= 17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom= 4303 Step= 18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom= 4301 Step= 19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom= 4301 Step= 20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom= 4301 Step= 21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom= 4301 140,1 . . . . -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Minimization Error
Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those? Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkulwrote: > > > On 10/19/17 8:21 PM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> Thank you very much for the reply. My concern is "step 11: One or more >> water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate". What >> should I do to avoid it? >> > > That happens often during minimization, especially the early steps. If it > doesn't come back up again, it's fine. It should never happen during MD. > > -Justin > > > Thank you. >> >> On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul wrote: >> >> >>> On 10/19/17 8:10 PM, Amali Guruge wrote: >>> >>> Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water
Re: [gmx-users] Energy Minimization Error
On 10/19/17 8:21 PM, Amali Guruge wrote: Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? That happens often during minimization, especially the early steps. If it doesn't come back up again, it's fine. It should never happen during MD. -Justin Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkulwrote: On 10/19/17 8:10 PM, Amali Guruge wrote: Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. mdrun stopped after 2000 steps because you told it to. You need to minimize further, so increase nsteps (or set it to -1 to let mdrun go as long as it needs to without having to guess a number). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe
Re: [gmx-users] Energy Minimization Error
Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkulwrote: > > > On 10/19/17 8:10 PM, Amali Guruge wrote: > >> Dear Gromacs Users, >> >> I tried to energy minimize my system using the steep integrator. However, >> it gave the following message. >> >> Steepest Descents: >> Tolerance (Fmax) = 5.0e+02 >> Number of steps= 2000 >> Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= >> 14611 >> Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= >> 18527 >> Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= >> 1005 >> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= >> 6994 >> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= >> 58902 >> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= >> 515 >> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= >> 188631 >> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= >> 188631 >> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= >> 188631 >> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= >> 188631 >> Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= >> 188631 >> >> step 11: One or more water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> After 2000 steps it says, >> >> Steepest Descents did not converge to Fmax < 500 in 2001 steps. >> Potential Energy = -4.6310655e+06 >> Maximum force = 6.7453154e+03 on atom 18769 >> Norm of force = 3.3632809e+01 >> >> Simulation ended prematurely, no performance report will be written. >> >> >> my em.mdp file contains following parameters. >> >> integrator= steep; simulation algorithm >> dt= 0.002; time step (ps) >> nsteps= 2000; # steps >> comm_mode= linear; c.o.m. motion reset >> ; >> ;Energy Minimization >> emtol= 500; converged F lt value (kJ mol-1 nm-1) >> emstep= 0.01 ; initial step size (nm) >> ; >> ;Output Control >> nstxout= 5 ; write coordinates to .trr >> nstvout= 5; write velocities to .trr >> nstlog= 5; write energies to .log >> nstenergy= 1; write energies to .edr >> ; >> ;Neightbour Searching >> cutoff-scheme = Verlet; scheme used for >> generating pair list >> nstlist = 10 ; update neighbour list >> ns_type= grid; neighbour list method >> pbc= xyz; periodic boundary conditions >> rlist= 0.9 ; cut-off for short-range neighbour >> (nm) >> ; >> ;Electrostatics and VdW >> coulombtype= PME; type of coulomb interaction >> rcoulomb= 0.9; cut-off distance for coulomb >> epsilon_r= 1; dielectric constant >> rvdw= 0.9; cut-off for vdw >> fourierspacing= 0.12; maximum grid spacing for FFT >> pme_order= 4; interpolation order for PME >> ewald_rtol= 1e-5; relative strength of Ewald-shifted >> DispCorr= EnerPres ; long range dispersion >> corrections >> ; >> ;Temperature Coupling >> Tcoupl= no; type of temperature coupling >> ; >> ;Pressure Coupling >> Pcoupl= no ; type of pressure coupling >> ; >> ;Velocity Generation >> gen_vel= no ; generate initial velocities >> ; >> ;Bonds >> constraints= none; bond constraint type >> >> I used gmx solvate to add water molecules to the system. >> >> How could I get rid of bad contacts of water molecules? Appreciate if >> anyone help me to solve the problem. >> > > mdrun stopped after 2000 steps because you told it to. You need to > minimize further, so increase nsteps (or set it to -1 to let mdrun go as > long as it needs to without having to guess a number). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support >
Re: [gmx-users] Energy Minimization Error
On 10/19/17 8:10 PM, Amali Guruge wrote: Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. mdrun stopped after 2000 steps because you told it to. You need to minimize further, so increase nsteps (or set it to -1 to let mdrun go as long as it needs to without having to guess a number). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy Minimization Error
Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. Thank you. Sincerely, A Guruge -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization issue
On 10/16/17 5:19 AM, Khadija Amine wrote: Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has stopped, but the forces have not converged to the* *requested precision Fmax < 1000 (which may not be possible for your system).* *It stopped because the algorithm tried to make a new step whose size was too* *small, or there was no change in the energy since last step. Either way, we* *regard the minimization as converged to within the available machine* *precision, given your starting configuration and EM parameters* *Double precision normally gives you higher accuracy, but this is often not* *needed for preparing to run molecular dynamics.* *You might need to increase your constraint accuracy, or turn* *off constraints altogether (set constraints = none in mdp file)* Could you please tell me what is the issue and provide some suggestions http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization issue
Dear Gromacs users, I'm simulation a double chain protein-ligand complex using Amber force field. I have written parameters and generated the topology. The energy minimization of the complex gives me the following error: *Energy minimization has stopped, but the forces have not converged to the* *requested precision Fmax < 1000 (which may not be possible for your system).* *It stopped because the algorithm tried to make a new step whose size was too* *small, or there was no change in the energy since last step. Either way, we* *regard the minimization as converged to within the available machine* *precision, given your starting configuration and EM parameters* *Double precision normally gives you higher accuracy, but this is often not* *needed for preparing to run molecular dynamics.* *You might need to increase your constraint accuracy, or turn* *off constraints altogether (set constraints = none in mdp file)* Could you please tell me what is the issue and provide some suggestions Thank you *Best regards* *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] ENERGY MINIMIZATION
Hi, In a cygwin terminal, having source'd GMXRC (see the install guide), just like you need to do under Linux. Mark On Tue, Jan 10, 2017 at 7:29 PM Subashini .Kwrote: > Hi Gromacs users, > > > I have installed gromacs in windows 7, 64 bit using cgywin. > > > I want to use the em.mdp file to grompp and generate a .tpr file. > > > In which terminal should the following commands be executed? > > > ; to test > ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v > ; mdrun -v -deffnm em > > Can someone tell me? > > > Thanks, > > Subashini.K > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ENERGY MINIMIZATION
Hi Gromacs users, I have installed gromacs in windows 7, 64 bit using cgywin. I want to use the em.mdp file to grompp and generate a .tpr file. In which terminal should the following commands be executed? ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v -deffnm em Can someone tell me? Thanks, Subashini.K -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization steps
Thank you Alex and Mark for your replies. :-) Azeem > Hi, > > How many steps does it take you to walk down a mountain to a certain > village? :-) Depends where you are on the mountain, and what's in the way. > But if all you need is to be somewhere near the valley floor to start > equilibration, anything goes! > > Mark > > On Wed, 21 Dec 2016 17:11 Alexwrote: > >> This isn't a Gromacs-specific parameter, or, for that matter, anything >> that straightforwardly depends on the nature of the system >> (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial >> cases. The max number of minimization steps is something that limits an >> energy minimization attempt, given the minimization algorithm, >> tolerance, the energy step, and, of course, how well-behaved you expect >> your system to be. It is a reasonable trial and error guess aimed at >> computational efficiency, e.g. not exceeding a certain amount of >> computational burden for really bad structures. Alternatively, limiting >> the number of minimization steps can help not produce some kind of a >> freaky structure when you have several local minima nearby. >> >> >> Alex >> >> >> On 12/20/2016 10:51 PM, Syed Azeem wrote: >> > Hi all, >> > >> > What is the basis of inputting the maximum number of energy >> > minimization steps in GROMACS? >> > Does maximum number of energy minimization steps depend on the number >> > of residues? >> > >> > I came across many articles wherein the authors have described the >> > number of energy minimization steps within which they have minimized >> > their protein. >> > >> > I have a protein of 596 residues to be simulated. >> > >> > Thanks in advance >> > >> > Azeem >> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization steps
Hi, How many steps does it take you to walk down a mountain to a certain village? :-) Depends where you are on the mountain, and what's in the way. But if all you need is to be somewhere near the valley floor to start equilibration, anything goes! Mark On Wed, 21 Dec 2016 17:11 Alexwrote: > This isn't a Gromacs-specific parameter, or, for that matter, anything > that straightforwardly depends on the nature of the system > (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial > cases. The max number of minimization steps is something that limits an > energy minimization attempt, given the minimization algorithm, > tolerance, the energy step, and, of course, how well-behaved you expect > your system to be. It is a reasonable trial and error guess aimed at > computational efficiency, e.g. not exceeding a certain amount of > computational burden for really bad structures. Alternatively, limiting > the number of minimization steps can help not produce some kind of a > freaky structure when you have several local minima nearby. > > > Alex > > > On 12/20/2016 10:51 PM, Syed Azeem wrote: > > Hi all, > > > > What is the basis of inputting the maximum number of energy > > minimization steps in GROMACS? > > Does maximum number of energy minimization steps depend on the number > > of residues? > > > > I came across many articles wherein the authors have described the > > number of energy minimization steps within which they have minimized > > their protein. > > > > I have a protein of 596 residues to be simulated. > > > > Thanks in advance > > > > Azeem > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization steps
This isn't a Gromacs-specific parameter, or, for that matter, anything that straightforwardly depends on the nature of the system (solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial cases. The max number of minimization steps is something that limits an energy minimization attempt, given the minimization algorithm, tolerance, the energy step, and, of course, how well-behaved you expect your system to be. It is a reasonable trial and error guess aimed at computational efficiency, e.g. not exceeding a certain amount of computational burden for really bad structures. Alternatively, limiting the number of minimization steps can help not produce some kind of a freaky structure when you have several local minima nearby. Alex On 12/20/2016 10:51 PM, Syed Azeem wrote: Hi all, What is the basis of inputting the maximum number of energy minimization steps in GROMACS? Does maximum number of energy minimization steps depend on the number of residues? I came across many articles wherein the authors have described the number of energy minimization steps within which they have minimized their protein. I have a protein of 596 residues to be simulated. Thanks in advance Azeem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization steps
Hi all, What is the basis of inputting the maximum number of energy minimization steps in GROMACS? Does maximum number of energy minimization steps depend on the number of residues? I came across many articles wherein the authors have described the number of energy minimization steps within which they have minimized their protein. I have a protein of 596 residues to be simulated. Thanks in advance Azeem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Minimization
On 11/3/16 10:11 AM, Mishelle Oña wrote: Positive values of potential energy and I am in vacuo. Your outcome is exactly what you should expect. Energies can be positive, and almost always are when doing work in vacuo. The net negative energy in condensed phase is driven by attractive solute-solvent and solvent-solvent interactions, of which you have none in the gas phase. -Justin Mishelle Sent from my Samsung device Original message From: Justin Lemkul <jalem...@vt.edu> Date: 11/03/2016 08:43 (GMT-05:00) To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Minimization On 11/2/16 9:40 PM, Mishelle Oña wrote: Hello I have a question about energy minimization tool. I am modelling a polymer and I use a force field I have developed. I have run a EM and got positive values. Can you help me with this? Positive values for what? Are you in vacuo or in solvent? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Minimization
Positive values of potential energy and I am in vacuo. Mishelle Sent from my Samsung device Original message From: Justin Lemkul <jalem...@vt.edu> Date: 11/03/2016 08:43 (GMT-05:00) To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Energy Minimization On 11/2/16 9:40 PM, Mishelle Oña wrote: > Hello > > I have a question about energy minimization tool. I am modelling a polymer > and I use a force field I have developed. I have run a EM and got positive > values. Can you help me with this? > Positive values for what? Are you in vacuo or in solvent? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Minimization
On 11/2/16 9:40 PM, Mishelle Oña wrote: Hello I have a question about energy minimization tool. I am modelling a polymer and I use a force field I have developed. I have run a EM and got positive values. Can you help me with this? Positive values for what? Are you in vacuo or in solvent? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy Minimization
Hello I have a question about energy minimization tool. I am modelling a polymer and I use a force field I have developed. I have run a EM and got positive values. Can you help me with this? Best regards, Mishelle -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Hi Surya, I'm not sure I understand what you want to do. Do you want to energy minimise an entire trajectory? After the production phase? Why? The -c flag in mdrun is the output, the last conformation sampled during the mdrun. You can use this output file as the input structure for an energy minimisation (-c option in grompp to prepare the .tpr file), I just don't see the point in doing that. Also, -c flag in grompp doesn't accept .xtc files. If you type "grompp -h" you'll see that. Cheers, On 28 September 2016 at 05:53, Seera Suryanarayanawrote: > Dear gromacs users, > I have done simulations for 100ns. I would like to do energy minimization > by using trajectory file which I got after production phase. Can I do > energy minimization passing the trajectory file to -c argument? If it is > yes, then tell me how to do it. > > Thanks in advance > > Surya > Graduate student > India. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -- Catarina A. Carvalheda PhD Student Computational Biology Division SLS & SSE University of Dundee DD1 5EH, Dundee, Scotland, UK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Dear gromacs users, I have done simulations for 100ns. I would like to do energy minimization by using trajectory file which I got after production phase. Can I do energy minimization passing the trajectory file to -c argument? If it is yes, then tell me how to do it. Thanks in advance Surya Graduate student India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization, of peptide-ligand, tearing peptide apart
Hi everyone I am currently trying to perform a peptide-ligand (~4000 and 110 Da respectively) simulated annealing study using gromacs (5.1.2) with Amber force fields. Under the initial energy minimization step (minim.mdp and nvt.mdp) I am finding that the step fails. It then kicks out pdb files, which when opened depicts a ligand that has 'exploded' with the peptide fragmented into a number of pieces. Under the same conditions, I can get the peptide to run with a ligand about twice the size of the above, which follows through to completion of all annealing steps to gain output pdb files. Accounting for a peptide only system, the peptide will also follow through to completion. Is anyone able to suggest how to optimize the minim/nvt files, or make sense of the log file. I have linked to the minim, nvt and output log files below. minim https://www.dropbox.com/s/80wwe8n2ncpg77t/minim.mdp?dl=0 nvt https://www.dropbox.com/s/qruyanl8vg1a3no/nvt.mdp?dl=0 Log details (md_temp.e20786725) https://www.dropbox.com/s/0fnjm05ub85yiun/md_temp_e20786725.txt?dl=0 Any help would be greatly appreciated. Richard -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization has stopped
Thanks a lot Justinn and Mark for the valuable suggestions. I will start over again by choosing a force field which is suitable for the RNA molecules. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:55 PM, Justin Lemkulwrote: > > > On 6/23/16 7:17 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> The main aim of the study is to study the interaction between a polymer >> (chitosan) and RNA molecules by simulating them togather. I have already >> successfully simulated my polymer system using OPLS AA force field. >> >> To simulate them together I need to write the OPLS AA parameters for RNA >> molecules. I was suggested (Link Below) earlier that I can take the >> charges >> from any other forcefield. >> >> (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) >> >> please enlight me where I am going wrong. >> >> > I think you misunderstood what I said in that thread. > > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html > > "You should find force field parameters specifically for the base from > published literature or from another force field." > > This means: find a force field that has parametrized the species you need > and use it. This does not mean: hack together something from "any other > force field" you like and try to make it OPLS-AA. You did not say before > that you were dealing with a complex system like this. You just said your > guanine charges didn't add up. So I addressed that problem. > > Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an > invalid approach. > > Pick a force field. Use that force field. Do not try to kludge together > some hybrid entity. Force fields are designed to be internally > self-consistent. If you do not have a proper balance of interactions, you > are not doing a useful simulation. You are generating random numbers. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization has stopped
On 6/23/16 7:17 AM, Anurag Dobhal wrote: Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. I think you misunderstood what I said in that thread. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-June/106520.html "You should find force field parameters specifically for the base from published literature or from another force field." This means: find a force field that has parametrized the species you need and use it. This does not mean: hack together something from "any other force field" you like and try to make it OPLS-AA. You did not say before that you were dealing with a complex system like this. You just said your guanine charges didn't add up. So I addressed that problem. Putting CHARMM27 charges into the OPLS-AA force field is unequivocally an invalid approach. Pick a force field. Use that force field. Do not try to kludge together some hybrid entity. Force fields are designed to be internally self-consistent. If you do not have a proper balance of interactions, you are not doing a useful simulation. You are generating random numbers. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization has stopped
Hi, You were recommended to pick a force field, not to combine parts of force fields. Choosing to simulate your polymer OPLS/AA if you then want to combine with RNA is not a good experimental design, unless you can do the combined simulation also in OPLS/AA. I would repeat the polymer experiment in whatever forcefield is also good for the experiment with RNA. Mark On Thu, Jun 23, 2016 at 1:18 PM Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Dear Justin, > > The main aim of the study is to study the interaction between a polymer > (chitosan) and RNA molecules by simulating them togather. I have already > successfully simulated my polymer system using OPLS AA force field. > > To simulate them together I need to write the OPLS AA parameters for RNA > molecules. I was suggested (Link Below) earlier that I can take the charges > from any other forcefield. > > (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) > > please enlight me where I am going wrong. > > Thank You > > > > > > > > > *Anurag Dobhal* > *Graduate Student (Bioprocess Technology)* > *Institute of Chemical Technology, Mumbai* > *Contact: +91 8898486877* > > > On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkulwrote: > > > > > > > On 6/23/16 7:00 AM, Anurag Dobhal wrote: > > > >> I am using OPLS AA force field. parameters (charges) for the atoms are > >> taken from the charmm27 force field. > >> > >> > > So, by using some hybridized force field, you can't successfully minimize > > a structure. That should tell you something. Why are you trying to do > > this, and what leads you to believe that some hybrid OPLS/CHARMM > > combination is even sensible? You can't just mix the charges from one > > force field with another to create some kind of Frankenforcefield. > > > > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly > > optimized for RNA simulations. > > > > -Justin > > > > > >> > >> > >> *Anurag Dobhal* > >> *Graduate Student (Bioprocess Technology)* > >> *Institute of Chemical Technology, Mumbai* > >> *Contact: +91 8898486877* > >> > >> > >> > >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: > >> > >> > >>> > >>> On 6/23/16 6:44 AM, Justin Lemkul wrote: > >>> > >>> > > On 6/23/16 6:35 AM, Anurag Dobhal wrote: > > Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA > force > > field. I have written parameters using CHARMM27 force field for RNA > > molecules. > > > > > > What does this mean? Are you using OPLS-AA or CHARMM27? > > > Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly > >>> superior for RNA. > >>> > >>> -Justin > >>> > >>> > >>> Minimising the molecule by invoking mdrun gives me the follwoing error. > >>> > > > Energy minimization has stopped, but the forces have not converged to > > the > > requested precision Fmax < 1000 (which may not be possible for your > > system). > > It stopped because the algorithm tried to make a new step whose size > > was > > too > > small, or there was no change in the energy since last step. Either > > way, > > we > > regard the minimization as converged to within the available machine > > precision, given your starting configuration and EM parameters. > > > > Double precision normally gives you higher accuracy, but this is > often > > not > > needed for preparing to run molecular dynamics. > > You might need to increase your constraint accuracy, or turn > > off constraints altogether (set constraints = none in mdp file) > > > > > > > > > - > > > > The contents of the .mdp file are the following > > > > ; minim.mdp - used as input into grompp to generate em.tpr > > integrator = steep ; Algorithm (steep = steepest descent > minimization) > > emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 > > kJ/mol/nm > > emstep = 0.01 ; Energy step size > > nsteps = 5 ; Maximum number of (minimization) steps to perform > > > > ; Parameters describing how to find the neighbors of each atom and > how > > to > > calculate the interactions > > nstlist= 1; Frequency to update the neighbor list and long > > range > > forces > > cutoff-scheme = Verlet > > ns_type= grid ; Method to determine neighbor list (simple, grid) > > coulombtype= PME ; Treatment of long range electrostatic > > interactions > > rcoulomb= 1.0 ; Short-range electrostatic cut-off > > rvdw= 1.0 ; Short-range Van der Waals cut-off > > pbc= xyz ; Periodic Boundary Conditions (yes/no) > > > > any suggestions ? > > > > > > > > >
Re: [gmx-users] Energy minimization has stopped
Dear Justin, The main aim of the study is to study the interaction between a polymer (chitosan) and RNA molecules by simulating them togather. I have already successfully simulated my polymer system using OPLS AA force field. To simulate them together I need to write the OPLS AA parameters for RNA molecules. I was suggested (Link Below) earlier that I can take the charges from any other forcefield. (http://permalink.gmane.org/gmane.science.biology.gromacs.user/85228) please enlight me where I am going wrong. Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:33 PM, Justin Lemkulwrote: > > > On 6/23/16 7:00 AM, Anurag Dobhal wrote: > >> I am using OPLS AA force field. parameters (charges) for the atoms are >> taken from the charmm27 force field. >> >> > So, by using some hybridized force field, you can't successfully minimize > a structure. That should tell you something. Why are you trying to do > this, and what leads you to believe that some hybrid OPLS/CHARMM > combination is even sensible? You can't just mix the charges from one > force field with another to create some kind of Frankenforcefield. > > Recent RNA force fields like CHARMM36 and recent AMBER updates are highly > optimized for RNA simulations. > > -Justin > > >> >> >> *Anurag Dobhal* >> *Graduate Student (Bioprocess Technology)* >> *Institute of Chemical Technology, Mumbai* >> *Contact: +91 8898486877* >> >> >> >> On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/23/16 6:44 AM, Justin Lemkul wrote: >>> >>> On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force > field. I have written parameters using CHARMM27 force field for RNA > molecules. > > > What does this mean? Are you using OPLS-AA or CHARMM27? Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly >>> superior for RNA. >>> >>> -Justin >>> >>> >>> Minimising the molecule by invoking mdrun gives me the follwoing error. >>> > Energy minimization has stopped, but the forces have not converged to > the > requested precision Fmax < 1000 (which may not be possible for your > system). > It stopped because the algorithm tried to make a new step whose size > was > too > small, or there was no change in the energy since last step. Either > way, > we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often > not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > > > - > > The contents of the .mdp file are the following > > ; minim.mdp - used as input into grompp to generate em.tpr > integrator = steep ; Algorithm (steep = steepest descent minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 > kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps = 5 ; Maximum number of (minimization) steps to perform > > ; Parameters describing how to find the neighbors of each atom and how > to > calculate the interactions > nstlist= 1; Frequency to update the neighbor list and long > range > forces > cutoff-scheme = Verlet > ns_type= grid ; Method to determine neighbor list (simple, grid) > coulombtype= PME ; Treatment of long range electrostatic > interactions > rcoulomb= 1.0 ; Short-range electrostatic cut-off > rvdw= 1.0 ; Short-range Van der Waals cut-off > pbc= xyz ; Periodic Boundary Conditions (yes/no) > > any suggestions ? > > > http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -Justin -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>>
Re: [gmx-users] Energy minimization has stopped
On 6/23/16 7:00 AM, Anurag Dobhal wrote: I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. So, by using some hybridized force field, you can't successfully minimize a structure. That should tell you something. Why are you trying to do this, and what leads you to believe that some hybrid OPLS/CHARMM combination is even sensible? You can't just mix the charges from one force field with another to create some kind of Frankenforcefield. Recent RNA force fields like CHARMM36 and recent AMBER updates are highly optimized for RNA simulations. -Justin *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkulwrote: On 6/23/16 6:44 AM, Justin Lemkul wrote: On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly superior for RNA. -Justin Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization has stopped
I am using OPLS AA force field. parameters (charges) for the atoms are taken from the charmm27 force field. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Jun 23, 2016 at 4:15 PM, Justin Lemkulwrote: > > > On 6/23/16 6:44 AM, Justin Lemkul wrote: > >> >> >> On 6/23/16 6:35 AM, Anurag Dobhal wrote: >> >>> Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force >>> field. I have written parameters using CHARMM27 force field for RNA >>> molecules. >>> >>> >> What does this mean? Are you using OPLS-AA or CHARMM27? >> >> > Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly > superior for RNA. > > -Justin > > > Minimising the molecule by invoking mdrun gives me the follwoing error. >>> >>> Energy minimization has stopped, but the forces have not converged to the >>> requested precision Fmax < 1000 (which may not be possible for your >>> system). >>> It stopped because the algorithm tried to make a new step whose size was >>> too >>> small, or there was no change in the energy since last step. Either way, >>> we >>> regard the minimization as converged to within the available machine >>> precision, given your starting configuration and EM parameters. >>> >>> Double precision normally gives you higher accuracy, but this is often >>> not >>> needed for preparing to run molecular dynamics. >>> You might need to increase your constraint accuracy, or turn >>> off constraints altogether (set constraints = none in mdp file) >>> >>> >>> - >>> >>> The contents of the .mdp file are the following >>> >>> ; minim.mdp - used as input into grompp to generate em.tpr >>> integrator = steep ; Algorithm (steep = steepest descent minimization) >>> emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 >>> kJ/mol/nm >>> emstep = 0.01 ; Energy step size >>> nsteps = 5 ; Maximum number of (minimization) steps to perform >>> >>> ; Parameters describing how to find the neighbors of each atom and how to >>> calculate the interactions >>> nstlist= 1; Frequency to update the neighbor list and long range >>> forces >>> cutoff-scheme = Verlet >>> ns_type= grid ; Method to determine neighbor list (simple, grid) >>> coulombtype= PME ; Treatment of long range electrostatic interactions >>> rcoulomb= 1.0 ; Short-range electrostatic cut-off >>> rvdw= 1.0 ; Short-range Van der Waals cut-off >>> pbc= xyz ; Periodic Boundary Conditions (yes/no) >>> >>> any suggestions ? >>> >>> >> >> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision >> >> >> mdrun prints which atom is feeling the maximum force, so that's a good >> place to >> start looking to see if there is an actual problem. >> >> -Justin >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization has stopped
On 6/23/16 6:44 AM, Justin Lemkul wrote: On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Also, if you are actually using CHARMM27, don't. CHARMM36 is vastly superior for RNA. -Justin Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization has stopped
On 6/23/16 6:35 AM, Anurag Dobhal wrote: Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. What does this mean? Are you using OPLS-AA or CHARMM27? Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision mdrun prints which atom is feeling the maximum force, so that's a good place to start looking to see if there is an actual problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization has stopped
Dear Gromacs Users, I am Simulating a RNA molecule using OPLS AA force field. I have written parameters using CHARMM27 force field for RNA molecules. Minimising the molecule by invoking mdrun gives me the follwoing error. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) - The contents of the .mdp file are the following ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid ; Method to determine neighbor list (simple, grid) coulombtype= PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) any suggestions ? *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
Hi, Thanks a lot for your time and patience. This time, I chose a very simple structure and then inspected the generated topology. The interesting point was that, there were some missing interactions. When I inspected them. I found that I had defined those interactions in ffbonded.itp file, but pdb2gmx has not assigned those definitions to these interactions. However, I added the appropriate gb_, ga_, or gd_ manually, and then performed the MD simulations and received an error as follows: Step= 210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= 46 Step= 212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= 44 Step= 216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= 46 Step= 218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= 44 Step= 221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= 46 Step= 224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= 44 Step= 227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= 46 Step= 229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= 44 Step= 232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= 46 Step= 234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= 44 Step= 235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= 46 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 100 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 236 steps, but did not reach the requested Fmax < 100. Potential Energy = -8.9157188e+04 Maximum force = 1.7089320e+05 on atom 44 Norm of force = 3.3110510e+03 gcq#220: "Let's Go Hang Out In a Mall" (LIVE) farideh@farideh-P61A-D3:~/multiple/G0$ you can access all the files via the following link: https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0 Truly yours, Farideh On Thu, Oct 22, 2015 at 11:24 AM, Mark Abrahamwrote: > Hi, > > Did you inspect your topology like I suggested? You need to know that there > are bonds exactly where you intend them, before doing any calculations with > them. > > Mark > > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Hi, > > > > I am trying to simulate a hyper-branched polymer (a dendrimer) in water. > > But, every time the system blows up at energy minimization step. > Therefore, > > according to what Mark had recommended I decided to start with a much > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had > > optimized it at M062x/6-31G* level, before starting the MD simulations. > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it > > residue by residue. After that, I started simulation procedure and > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any > > errors in energy minimization step, and the potential energy - EM step > plot > > was reasonable. But, when I loaded em.gro file in VMD, the structure was > > completely messed up as in G3 dendrimer. This time I continued the MD > > simulation until production MD, and there was no error. However, the > system > > is blown up. You can access all the simulation files, pdb structure, and > > the photos of G1 structure before and after EM step via: > > > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 > > > > Since I am a beginner in this area, I do not know what is the solution > for > > this problem. > > Do you think errors that occur during the G3 simulation are relevant to > the > > initial structure? > > any suggestion or recommendation is appreciated. > > > > Thanks in advance > > Farideh > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit >
Re: [gmx-users] energy minimization error
Hi, pdb2gmx and grompp are pretty talkative about things like missing parameters and bonds - go back and read what they had to say, and particularly what pdb2gmx thought about your specbonds. Mark On Fri, Oct 23, 2015 at 5:51 PM faride badalkhaniwrote: > Hi, > > Thanks a lot for your time and patience. This time, I chose a very simple > structure and then inspected the generated topology. The interesting point > was that, there were some missing interactions. When I inspected them. I > found that I had defined those interactions in ffbonded.itp file, but > pdb2gmx has not assigned those definitions to these interactions. However, > I added the appropriate gb_, ga_, or gd_ manually, and then performed the > MD simulations and received an error as follows: > > Step= 210, Dmax= 6.6e-03 nm, Epot= -8.80977e+04 Fmax= 1.48278e+05, atom= > 46 > Step= 212, Dmax= 4.0e-03 nm, Epot= -8.90453e+04 Fmax= 1.76644e+05, atom= > 44 > Step= 216, Dmax= 5.9e-04 nm, Epot= -8.90760e+04 Fmax= 1.48643e+05, atom= > 46 > Step= 218, Dmax= 3.6e-04 nm, Epot= -8.91295e+04 Fmax= 1.75349e+05, atom= > 44 > Step= 221, Dmax= 1.1e-04 nm, Epot= -8.91493e+04 Fmax= 1.48437e+05, atom= > 46 > Step= 224, Dmax= 3.2e-05 nm, Epot= -8.91556e+04 Fmax= 1.74146e+05, atom= > 44 > Step= 227, Dmax= 9.6e-06 nm, Epot= -8.91559e+04 Fmax= 1.51118e+05, atom= > 46 > Step= 229, Dmax= 5.8e-06 nm, Epot= -8.91570e+04 Fmax= 1.71312e+05, atom= > 44 > Step= 232, Dmax= 1.7e-06 nm, Epot= -8.91571e+04 Fmax= 1.54271e+05, atom= > 46 > Step= 234, Dmax= 1.0e-06 nm, Epot= -8.91572e+04 Fmax= 1.70893e+05, atom= > 44 > Step= 235, Dmax= 1.2e-06 nm, Epot= -8.91570e+04 Fmax= 1.57473e+05, atom= > 46 > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 100 (which may not be possible for your system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 236 steps, > but did not reach the requested Fmax < 100. > Potential Energy = -8.9157188e+04 > Maximum force = 1.7089320e+05 on atom 44 > Norm of force = 3.3110510e+03 > > gcq#220: "Let's Go Hang Out In a Mall" (LIVE) > > farideh@farideh-P61A-D3:~/multiple/G0$ > > you can access all the files via the following link: > https://www.dropbox.com/s/m1kxafyu1n749hb/G0.zip?dl=0 > > Truly yours, > Farideh > > On Thu, Oct 22, 2015 at 11:24 AM, Mark Abraham > wrote: > > > Hi, > > > > Did you inspect your topology like I suggested? You need to know that > there > > are bonds exactly where you intend them, before doing any calculations > with > > them. > > > > Mark > > > > On Thu, Oct 22, 2015 at 9:35 AM faride badalkhani < > > farideh.kham...@gmail.com> > > wrote: > > > > > Hi, > > > > > > I am trying to simulate a hyper-branched polymer (a dendrimer) in > water. > > > But, every time the system blows up at energy minimization step. > > Therefore, > > > according to what Mark had recommended I decided to start with a much > > > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I > had > > > optimized it at M062x/6-31G* level, before starting the MD simulations. > > > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it > > > residue by residue. After that, I started simulation procedure and > > > continued step by step. In spite of G3 PAMAM dendrimer I didn't face > any > > > errors in energy minimization step, and the potential energy - EM step > > plot > > > was reasonable. But, when I loaded em.gro file in VMD, the structure > was > > > completely messed up as in G3 dendrimer. This time I continued the MD > > > simulation until production MD, and there was no error. However, the > > system > > > is blown up. You can access all the simulation files, pdb structure, > and > > > the photos of G1 structure before and after EM step via: > > > > > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 > > > > > > Since I am a beginner in this area, I do not know what is the solution > > for > > > this problem. > > > Do you think errors that occur during the G3 simulation are relevant to > > the > > > initial structure? > > > any suggestion or recommendation is appreciated. > > > > > > Thanks in advance > > > Farideh > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > *
[gmx-users] energy minimization error
Hi, I am trying to simulate a hyper-branched polymer (a dendrimer) in water. But, every time the system blows up at energy minimization step. Therefore, according to what Mark had recommended I decided to start with a much smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had optimized it at M062x/6-31G* level, before starting the MD simulations. Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it residue by residue. After that, I started simulation procedure and continued step by step. In spite of G3 PAMAM dendrimer I didn't face any errors in energy minimization step, and the potential energy - EM step plot was reasonable. But, when I loaded em.gro file in VMD, the structure was completely messed up as in G3 dendrimer. This time I continued the MD simulation until production MD, and there was no error. However, the system is blown up. You can access all the simulation files, pdb structure, and the photos of G1 structure before and after EM step via: https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 Since I am a beginner in this area, I do not know what is the solution for this problem. Do you think errors that occur during the G3 simulation are relevant to the initial structure? any suggestion or recommendation is appreciated. Thanks in advance Farideh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
Hi, Did you inspect your topology like I suggested? You need to know that there are bonds exactly where you intend them, before doing any calculations with them. Mark On Thu, Oct 22, 2015 at 9:35 AM faride badalkhaniwrote: > Hi, > > I am trying to simulate a hyper-branched polymer (a dendrimer) in water. > But, every time the system blows up at energy minimization step. Therefore, > according to what Mark had recommended I decided to start with a much > smaller dendrimer (i.e. G1 PAMAM dendrimer) , rather than a G3 one. I had > optimized it at M062x/6-31G* level, before starting the MD simulations. > Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it > residue by residue. After that, I started simulation procedure and > continued step by step. In spite of G3 PAMAM dendrimer I didn't face any > errors in energy minimization step, and the potential energy - EM step plot > was reasonable. But, when I loaded em.gro file in VMD, the structure was > completely messed up as in G3 dendrimer. This time I continued the MD > simulation until production MD, and there was no error. However, the system > is blown up. You can access all the simulation files, pdb structure, and > the photos of G1 structure before and after EM step via: > > https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 > > Since I am a beginner in this area, I do not know what is the solution for > this problem. > Do you think errors that occur during the G3 simulation are relevant to the > initial structure? > any suggestion or recommendation is appreciated. > > Thanks in advance > Farideh > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization error
Hi, As you said, I started with a G1 PAMAM dendrimer, rather than a G3 one. I had optimized it at M062x/6-31G* level, before starting the MD simulations. Then, I generated .pdb file from .log (Gaussian 09) file, and sorted it residue by residue. After that, I started simulation procedure and continued step by step. In spite of G3 PAMAM dendrimer I didn't face any errors in energy minimization step, and the potential energy - EM step plot was reasonable. But, when I loaded em.gro file in VMD, the structure was completely messed up as in G3 dendrimer. This time I continued the MD simulation until production MD, and there was no error. However, the system is blown up. You can access all the simulation files, pdb structure, and the photos of G1 structure before and after EM step via: https://www.dropbox.com/s/sdggfaklg530hq0/G1.zip?dl=0 Since I am a beginner in this area, I do not know what is the solution for this problem. Do you think errors that occur during the G3 simulation are relevant to the initial structure? any suggestion or recommendation is appreciated. Thanks in advance Farideh On Sat, Oct 17, 2015 at 6:29 PM, Mark Abrahamwrote: > Hi, > > What some visualization program shows about bonds doesn't mean anything - > it has not parsed your topology. You have no option but to look at the .top > produced and reason about what it shows, but yours is very complex. I > strongly recommend starting with something simpler than a multiply branched > dendrimer. Join two units with a specbond, inspect the .top so that you > know it has what you think it has, and get that to EM and simulation > stably. Then you can get more complex. > > Mark > > On Sat, Oct 17, 2015 at 3:58 PM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Dear gromacs users, > > > > As I said before I faced with the minimization error, so I changed > > coordinates of atoms in pdb file, but the problem is the same. the only > > thing that changes in every run is atom number. I modified pdb for many > > times. > > > > Steepest Descents converged to Fmax < 1000 in 530 steps > > Potential Energy = -5.5180181e+05 > > Maximum force = 7.4496063e+02 on atom 501 > > Norm of force = 3.8248455e+01 > > > > > > Moreover gro structure was completely messed up when was visualized in > vmd. > > you can see the picture of my structure in below dropbox link: > > > > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 > > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 > > > > and this is the pdb file dropbox link: > > > > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 > > > > > > I used cg algorithm after steep for minimization, too. But it did not > work. > > is there any way to solve this problem? > > > > any help is appreciated. > > > > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > Look at atom 380 and see why the forces might be high. > > > > > > Mark > > > > > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > > > farideh.kham...@gmail.com> > > > wrote: > > > > > > > Thank you for your great help on specbond.dat file. I defined it and > I > > > > could go ahead until Energy minimization step. I have used this > > minim.mdp > > > > file > > > > > > > > ; minim.mdp - used as input into grompp to generate em.tpr > > > > ; Parameters describing what to do, when to stop and what to save > > > > integrator= steep; Algorithm (steep = steepest descent > > > > minimization) > > > > emtol = 1000.0 ; Stop minimization when the maximum > > force < > > > > 1000.0 kJ/mol/nm > > > > emstep = 0.01 ; Energy step size > > > > nsteps= 5 ; Maximum number of (minimization) > steps > > > to > > > > perform > > > > > > > > ; Parameters describing how to find the neighbors of each atom and > how > > to > > > > calculate the interactions > > > > nstlist = 1; Frequency to update the neighbor > list > > > and > > > > long range forces > > > > ns_type = grid; Method to determine neighbor list > > > > (simple, grid) > > > > rlist = 1.0; Cut-off for making neighbor list > > > > (short range forces) > > > > coulombtype= PME; Treatment of long range electrostatic > > > > interactions > > > > rcoulomb = 1.0; Short-range electrostatic cut-off > > > > rvdw = 1.0; Short-range Van der Waals cut-off > > > > pbc = xyz ; Periodic Boundary Conditions > > (yes/no) > > > > > > > > But when I run mdrun -v -deffnm em command, I get this error: > > > > > > > > Energy minimization has stopped, but the forces have not converged to > > the > > > > requested precision Fmax < 1000 (which may not be possible for your > > > > system). > > > > It stopped because the algorithm tried to make a new step whose size > > was > > > > too > > > > small, or there was no change
Re: [gmx-users] Energy minimization error
Dear gromacs users, As I said before I faced with the minimization error, so I changed coordinates of atoms in pdb file, but the problem is the same. the only thing that changes in every run is atom number. I modified pdb for many times. Steepest Descents converged to Fmax < 1000 in 530 steps Potential Energy = -5.5180181e+05 Maximum force = 7.4496063e+02 on atom 501 Norm of force = 3.8248455e+01 Moreover gro structure was completely messed up when was visualized in vmd. you can see the picture of my structure in below dropbox link: https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 and this is the pdb file dropbox link: https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 I used cg algorithm after steep for minimization, too. But it did not work. is there any way to solve this problem? any help is appreciated. On Mon, Oct 5, 2015 at 2:08 PM, Mark Abrahamwrote: > Hi, > > Look at atom 380 and see why the forces might be high. > > Mark > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > farideh.kham...@gmail.com> > wrote: > > > Thank you for your great help on specbond.dat file. I defined it and I > > could go ahead until Energy minimization step. I have used this minim.mdp > > file > > > > ; minim.mdp - used as input into grompp to generate em.tpr > > ; Parameters describing what to do, when to stop and what to save > > integrator= steep; Algorithm (steep = steepest descent > > minimization) > > emtol = 1000.0 ; Stop minimization when the maximum force < > > 1000.0 kJ/mol/nm > > emstep = 0.01 ; Energy step size > > nsteps= 5 ; Maximum number of (minimization) steps > to > > perform > > > > ; Parameters describing how to find the neighbors of each atom and how to > > calculate the interactions > > nstlist = 1; Frequency to update the neighbor list > and > > long range forces > > ns_type = grid; Method to determine neighbor list > > (simple, grid) > > rlist = 1.0; Cut-off for making neighbor list > > (short range forces) > > coulombtype= PME; Treatment of long range electrostatic > > interactions > > rcoulomb = 1.0; Short-range electrostatic cut-off > > rvdw = 1.0; Short-range Van der Waals cut-off > > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > > > But when I run mdrun -v -deffnm em command, I get this error: > > > > Energy minimization has stopped, but the forces have not converged to the > > requested precision Fmax < 1000 (which may not be possible for your > > system). > > It stopped because the algorithm tried to make a new step whose size was > > too > > small, or there was no change in the energy since last step. Either way, > we > > regard the minimization as converged to within the available machine > > precision, given your starting configuration and EM parameters. > > > > Double precision normally gives you higher accuracy, but this is often > not > > needed for preparing to run molecular dynamics. > > You might need to increase your constraint accuracy, or turn > > off constraints altogether (set constraints = none in mdp file) > > > > writing lowest energy coordinates. > > > > Steepest Descents converged to machine precision in 90 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -2.3956744e+05 > > Maximum force = 1.5824519e+05 on atom 380 > > Norm of force = 1.7695243e+03 > > > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > > > farideh@farideh-P61A-D3:~/FARIDEH$ > > > > I changed the emtol, emstep, and nsteps for a few times. However, I > > couldn't resolve this problem. Could you tell me if there is something > > wrong with the minim.mdp file? > > > > You can see all the files via: > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > > > Truly yours, > > Farideh > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] Energy minimization error
Hi, What some visualization program shows about bonds doesn't mean anything - it has not parsed your topology. You have no option but to look at the .top produced and reason about what it shows, but yours is very complex. I strongly recommend starting with something simpler than a multiply branched dendrimer. Join two units with a specbond, inspect the .top so that you know it has what you think it has, and get that to EM and simulation stably. Then you can get more complex. Mark On Sat, Oct 17, 2015 at 3:58 PM faride badalkhaniwrote: > Dear gromacs users, > > As I said before I faced with the minimization error, so I changed > coordinates of atoms in pdb file, but the problem is the same. the only > thing that changes in every run is atom number. I modified pdb for many > times. > > Steepest Descents converged to Fmax < 1000 in 530 steps > Potential Energy = -5.5180181e+05 > Maximum force = 7.4496063e+02 on atom 501 > Norm of force = 3.8248455e+01 > > > Moreover gro structure was completely messed up when was visualized in vmd. > you can see the picture of my structure in below dropbox link: > > https://www.dropbox.com/s/78v2cvii4gkd8ev/gro.bmp?dl=0 > https://www.dropbox.com/s/nyzyu3zmy1vvevg/pdb.bmp?dl=0 > > and this is the pdb file dropbox link: > > https://www.dropbox.com/s/yvxpl2igzi5ccad/120.pdb?dl=0 > > > I used cg algorithm after steep for minimization, too. But it did not work. > is there any way to solve this problem? > > any help is appreciated. > > On Mon, Oct 5, 2015 at 2:08 PM, Mark Abraham > wrote: > > > Hi, > > > > Look at atom 380 and see why the forces might be high. > > > > Mark > > > > On Mon, Oct 5, 2015 at 10:15 AM faride badalkhani < > > farideh.kham...@gmail.com> > > wrote: > > > > > Thank you for your great help on specbond.dat file. I defined it and I > > > could go ahead until Energy minimization step. I have used this > minim.mdp > > > file > > > > > > ; minim.mdp - used as input into grompp to generate em.tpr > > > ; Parameters describing what to do, when to stop and what to save > > > integrator= steep; Algorithm (steep = steepest descent > > > minimization) > > > emtol = 1000.0 ; Stop minimization when the maximum > force < > > > 1000.0 kJ/mol/nm > > > emstep = 0.01 ; Energy step size > > > nsteps= 5 ; Maximum number of (minimization) steps > > to > > > perform > > > > > > ; Parameters describing how to find the neighbors of each atom and how > to > > > calculate the interactions > > > nstlist = 1; Frequency to update the neighbor list > > and > > > long range forces > > > ns_type = grid; Method to determine neighbor list > > > (simple, grid) > > > rlist = 1.0; Cut-off for making neighbor list > > > (short range forces) > > > coulombtype= PME; Treatment of long range electrostatic > > > interactions > > > rcoulomb = 1.0; Short-range electrostatic cut-off > > > rvdw = 1.0; Short-range Van der Waals cut-off > > > pbc = xyz ; Periodic Boundary Conditions > (yes/no) > > > > > > But when I run mdrun -v -deffnm em command, I get this error: > > > > > > Energy minimization has stopped, but the forces have not converged to > the > > > requested precision Fmax < 1000 (which may not be possible for your > > > system). > > > It stopped because the algorithm tried to make a new step whose size > was > > > too > > > small, or there was no change in the energy since last step. Either > way, > > we > > > regard the minimization as converged to within the available machine > > > precision, given your starting configuration and EM parameters. > > > > > > Double precision normally gives you higher accuracy, but this is often > > not > > > needed for preparing to run molecular dynamics. > > > You might need to increase your constraint accuracy, or turn > > > off constraints altogether (set constraints = none in mdp file) > > > > > > writing lowest energy coordinates. > > > > > > Steepest Descents converged to machine precision in 90 steps, > > > but did not reach the requested Fmax < 1000. > > > Potential Energy = -2.3956744e+05 > > > Maximum force = 1.5824519e+05 on atom 380 > > > Norm of force = 1.7695243e+03 > > > > > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > > > > > farideh@farideh-P61A-D3:~/FARIDEH$ > > > > > > I changed the emtol, emstep, and nsteps for a few times. However, I > > > couldn't resolve this problem. Could you tell me if there is something > > > wrong with the minim.mdp file? > > > > > > You can see all the files via: > > > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > > > > > Truly yours, > > > Farideh > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > >
[gmx-users] Energy minimization error
Thank you for your great help on specbond.dat file. I defined it and I could go ahead until Energy minimization step. I have used this minim.mdp file ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1; Frequency to update the neighbor list and long range forces ns_type = grid; Method to determine neighbor list (simple, grid) rlist = 1.0; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb = 1.0; Short-range electrostatic cut-off rvdw = 1.0; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) But when I run mdrun -v -deffnm em command, I get this error: Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 1000 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 90 steps, but did not reach the requested Fmax < 1000. Potential Energy = -2.3956744e+05 Maximum force = 1.5824519e+05 on atom 380 Norm of force = 1.7695243e+03 gcq#187: "Been There, Done It" (Beavis and Butthead) farideh@farideh-P61A-D3:~/FARIDEH$ I changed the emtol, emstep, and nsteps for a few times. However, I couldn't resolve this problem. Could you tell me if there is something wrong with the minim.mdp file? You can see all the files via: https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization error
Hi, Look at atom 380 and see why the forces might be high. Mark On Mon, Oct 5, 2015 at 10:15 AM faride badalkhaniwrote: > Thank you for your great help on specbond.dat file. I defined it and I > could go ahead until Energy minimization step. I have used this minim.mdp > file > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > integrator= steep; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.01 ; Energy step size > nsteps= 5 ; Maximum number of (minimization) steps to > perform > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1; Frequency to update the neighbor list and > long range forces > ns_type = grid; Method to determine neighbor list > (simple, grid) > rlist = 1.0; Cut-off for making neighbor list > (short range forces) > coulombtype= PME; Treatment of long range electrostatic > interactions > rcoulomb = 1.0; Short-range electrostatic cut-off > rvdw = 1.0; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > But when I run mdrun -v -deffnm em command, I get this error: > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 1000 (which may not be possible for your > system). > It stopped because the algorithm tried to make a new step whose size was > too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 90 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -2.3956744e+05 > Maximum force = 1.5824519e+05 on atom 380 > Norm of force = 1.7695243e+03 > > gcq#187: "Been There, Done It" (Beavis and Butthead) > > farideh@farideh-P61A-D3:~/FARIDEH$ > > I changed the emtol, emstep, and nsteps for a few times. However, I > couldn't resolve this problem. Could you tell me if there is something > wrong with the minim.mdp file? > > You can see all the files via: > https://www.dropbox.com/s/sq2c103yxi4mc28/Farideh.zip?dl=0 > > Truly yours, > Farideh > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi; I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization
Hi;I've alreadyconverted the amber topology and coordinate files to gromacs format.But when I want to start running theenergy minimization first by using the grompp to generate .tpr file,I get this error: Program gmx, VERSION5.0.2Source code file:/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/toppush.c,line: 1353 Fatal error:Atomtype IP notfoundFor more informationand tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors I think that itcannot recognize the atoms. I don't know how to fix it. Best regards, Mohammad. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization
On 7/8/15 8:03 PM, Malihe Hasanzadeh wrote: Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not equilibrated well and blowing up! I chcked my em.pdb file and I saw the Sol box is separated from protein and DNA! This is probably just a PBC effect; use trjconv. Could you please help me, what should I do?what part of my set is wrong? Your EM outcome suggests an unresolvable clash in the system, so it's pointless to try dynamics unless you get a force below the specified tolerance (or at least of some other reasonable magnitude). mdrun tells you where the maximum force is, so that's where you should start looking. Beyond that, you'll have to give us a complete description of what you've done to prepare the system, parametrize the ligand, etc. General troubleshooting that you should always follow: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System my em.mdp: define = -DFLEXIBLE I'm assuming you're trying to use rigid water during the subsequent dynamics (you should), so you'll want to re-minimize without flexible water. Occasionally, the waters distort and SETTLE cannot fix the geometry. This is not likely the source of your problem, just an FYI. -Justin integrator = cg ; steep nsteps = 4000 nstlist = 1 constraints = none emtol = 100.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 nstcalcenergy = 1.2 ewald_rtol = 1e-05 coulombtype = PME cutoff-scheme = Group ns_type = grid rlist = 1.4 rcoulomb =1.4 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes Sincerely, Malihe -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization
Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not equilibrated well and blowing up! I chcked my em.pdb file and I saw the Sol box is separated from protein and DNA! Could you please help me, what should I do?what part of my set is wrong? my em.mdp: define = -DFLEXIBLE integrator = cg ; steep nsteps = 4000 nstlist = 1 constraints = none emtol = 100.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 nstcalcenergy = 1.2 ewald_rtol = 1e-05 coulombtype = PME cutoff-scheme = Group ns_type = grid rlist = 1.4 rcoulomb =1.4 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes Sincerely, Malihe -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * *Cheers* *James* On Sat, Jun 27, 2015 at 11:19 AM, James Lord jjamesgreen...@gmail.com wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
On 6/27/15 2:29 AM, James Lord wrote: Hi Justin For now I used *mdrun -nt 1* * and got rid of this error so hopefully the simulation wont crash. * The DD errors have nothing to do with physical stability; you just can't necessarily parallelize any arbitrary system over any arbitrary number of cores (DD cells). You can also parallelize with OpenMP to get some speed-up (mdrun -ntmpi 1 -ntomp N). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
On 6/26/15 7:19 PM, James Lord wrote: Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing There's nothing I can do with a topology that's a series of #include statements. Please also remind me what this is all about so I don't have to go digging through the archives for something from a month ago. Lots of things have happened since then :) -Justin Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
Hi Justin, I have asked this before, but this time I started up from scratch and used the input files that I know they are fine but again I am getting this error, Would you please tell me what is wrong in my topology files and where about in .top files the bond length are defined? https://drive.google.com/file/d/0B0YMTXH1gmQsbkpjTU9tWGFkSDA/view?usp=sharing Cheers James On Mon, May 18, 2015 at 1:13 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] energy minimization problem
Hi, I am simulating a 5X5 carbon nanotube in the presence of nucleic acids in Tip3P water. I have made this nanotube using VMD nanotube builder and made the topology using pdb2gmx. Upto the energy minimization step every thing was fine but when I proceed for energy minimization I get the carbon naotube crumpled when I view the em.gro file in VMD. It is worth mentioning that the nucleic acid remains unchanged during the em process and when I am going for NVT equilibration it does not produce any LINCS warning or stuffs like that. So is it happening because a visualization tool is unaware of the molecular topology or do I need to change some parameters in the em.mdp file? The cnt.itp file is as follows (partwise) ; File 'cnt.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat May 30 11:07:23 2015 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5.6 ; ; Command line was: ; pdb2gmx_d -f nishCNT.pdb -o init.gro -p cnt.top ; ; Force field was read from current directory or a relative path - path addeed [ moleculetype ] ; Namenrexcl SDG 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 SDG rtp SDG q 0.0 1 CA 0SDG C1 1 0 12.011 ; qtot 0 2 CA 0SDG C2 2 0 12.011 ; qtot 0 3 CA 0SDG C3 3 0 12.011 ; qtot 0 4 CA 0SDG C4 4 0 12.011 ; qtot 0 5 CA 0SDG C5 5 0 12.011 ; qtot 0 6 CA 0SDG C6 6 0 12.011 ; qtot 0 7 CA 0SDG C7 7 0 12.011 ; qtot 0 8 CA 0SDG C8 8 0 12.011 ; qtot 0 9 CA 0SDG C9 9 0 12.011 ; qtot 0 10 CA 0SDGC10 10 0 12.011 ; qtot 0 11 CA 0SDGC11 11 0 12.011 ; qtot 0 12 CA 0SDGC12 12 0 12.011 ; qtot 0 13 CA 0SDGC13 13 0 12.011 ; qtot 0 14 CA 0SDGC14 14 0 12.011 ; qtot 0 15 CA 0SDGC15 15 0 12.011 ; qtot 0 16 CA 0SDGC16 16 0 12.011 ; qtot 0 17 CA 0SDGC17 17 0 12.011 ; qtot 0 [ bonds ] ; aiaj funct b0 kb 1 2 1C6 H30.108 284512.0 1 6 1C5 H40.108 284512.0 1 403 1 0.108 284512.0 2 3 1C4 C70.1375 255224.0 2 385 1C370 C386 0.1375 255224.0 3 4 1C5 C100.1375 255224.0 3 7 1C8 C3690.1375 255224.0 4 5 1C6 C4000.1375 255224.0 5 400 1C383 C399 0.1375 255224.0 6 404 1 0.108 284512.0 7 8 1C9 C110.1375 255224.0 8 9 1C10 C14 0.1375 255224.0 811 1C12 C353 0.1375 255224.0 910 1C4 C3840.1375 255224.0 914 1C13 C368 0.1375 255224.0 1112 1C13 C15 0.1375 255224.0 11 353 1C338 C354 0.1375 255224.0 1213 1C14 C18 0.1375 255224.0 1215 1C16 C337 0.1375 255224.0 1318 1C17 C352 0.1375 255224.0 14 368 1C351 C367 0.1375 255224.0 1516 1C17 C19 0.1375 255224.0 15 337 1C322 C338 0.1375 255224.0 [ angles ] ; aiajak functth0 cthubo cub 2 1 6 5 120.00334.72 0.24162 29288.0 2 1 403 5 120.00251.04 0.21525 18409.6 6 1 403 5 120.00251.04 0.21525 18409.6 1 2 3 5 120.00334.72 0.24162 29288.0 1 2 385 5 120.00334.72 0.24162 29288.0 3 2 385 5 120.00334.72 0.24162 29288.0 2 3 4 5 120.00334.72 0.24162 29288.0 2 3 7 5 120.00334.72 0.24162 29288.0 4 3 7 5 120.00334.72 0.24162 29288.0 3 4 5 5
[gmx-users] energy minimization problem
Hi, The mdp file has pbc= xyz in the last line. In the previous mail it was written that pbc=full. Plaese ignore it. Thanks and regards Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
On 6/1/15 8:06 AM, soumadwip ghosh wrote: Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file? http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM I seem to have to post this information weekly... Here is how the CNT molecule looks like prior to energy minimization. pre energy min CNT https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing Yep, that's definitely wrong. I am not continuing any of the equilibration steps anymore. As you can see the CNT structure is distorted badly. Please help me out. What settings do I need to change in order to avoid such distortion? Is there a possibility that the cnt topology was wrong to begin with? The CNT topology is clearly wrong. It's probably missing some bonds or something. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
On 6/1/15 9:07 AM, soumadwip ghosh wrote: Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a possible way out. I don't see how that changes what I've said. You have a topology problem with the CNT. Simplify the system - build a smaller CNT, minimize it in vacuo, etc, then make it bigger/more complex. Look at the atoms that are distorting and check the existence of their bonded interactions and associated parameters. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
On 6/1/15 2:28 AM, soumadwip ghosh wrote: Hi, I am simulating a 5X5 carbon nanotube in the presence of nucleic acids in Tip3P water. I have made this nanotube using VMD nanotube builder and made the topology using pdb2gmx. Upto the energy minimization step every thing was fine but when I proceed for energy minimization I get the carbon naotube crumpled when I view the em.gro file in VMD. It is worth mentioning Please upload an image somewhere and provide the URL. that the nucleic acid remains unchanged during the em process and when I am going for NVT equilibration it does not produce any LINCS warning or stuffs like that. So is it happening because a visualization tool is unaware of the molecular topology or do I need to change some parameters in the em.mdp file? Possibly; see below. The cnt.itp file is as follows (partwise) Incomplete topologies are not generally useful. ; File 'cnt.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Sat May 30 11:07:23 2015 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx_d - VERSION 4.5.6 ; ; Command line was: ; pdb2gmx_d -f nishCNT.pdb -o init.gro -p cnt.top ; ; Force field was read from current directory or a relative path - path addeed [ moleculetype ] ; Namenrexcl SDG 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 0 SDG rtp SDG q 0.0 1 CA 0SDG C1 1 0 12.011 ; qtot 0 2 CA 0SDG C2 2 0 12.011 ; qtot 0 3 CA 0SDG C3 3 0 12.011 ; qtot 0 4 CA 0SDG C4 4 0 12.011 ; qtot 0 5 CA 0SDG C5 5 0 12.011 ; qtot 0 6 CA 0SDG C6 6 0 12.011 ; qtot 0 7 CA 0SDG C7 7 0 12.011 ; qtot 0 8 CA 0SDG C8 8 0 12.011 ; qtot 0 9 CA 0SDG C9 9 0 12.011 ; qtot 0 10 CA 0SDGC10 10 0 12.011 ; qtot 0 11 CA 0SDGC11 11 0 12.011 ; qtot 0 12 CA 0SDGC12 12 0 12.011 ; qtot 0 13 CA 0SDGC13 13 0 12.011 ; qtot 0 14 CA 0SDGC14 14 0 12.011 ; qtot 0 15 CA 0SDGC15 15 0 12.011 ; qtot 0 16 CA 0SDGC16 16 0 12.011 ; qtot 0 17 CA 0SDGC17 17 0 12.011 ; qtot 0 [ bonds ] ; aiaj funct b0 kb 1 2 1C6 H30.108 284512.0 1 6 1C5 H40.108 284512.0 1 403 1 0.108 284512.0 2 3 1C4 C70.1375 255224.0 2 385 1C370 C386 0.1375 255224.0 3 4 1C5 C100.1375 255224.0 3 7 1C8 C3690.1375 255224.0 4 5 1C6 C4000.1375 255224.0 5 400 1C383 C399 0.1375 255224.0 6 404 1 0.108 284512.0 7 8 1C9 C110.1375 255224.0 8 9 1C10 C14 0.1375 255224.0 811 1C12 C353 0.1375 255224.0 910 1C4 C3840.1375 255224.0 914 1C13 C368 0.1375 255224.0 1112 1C13 C15 0.1375 255224.0 11 353 1C338 C354 0.1375 255224.0 1213 1C14 C18 0.1375 255224.0 1215 1C16 C337 0.1375 255224.0 1318 1C17 C352 0.1375 255224.0 14 368 1C351 C367 0.1375 255224.0 1516 1C17 C19 0.1375 255224.0 15 337 1C322 C338 0.1375 255224.0 [ angles ] ; aiajak functth0 cthubo cub 2 1 6 5 120.00334.72 0.24162 29288.0 2 1 403 5 120.00251.04 0.21525 18409.6 6 1 403 5 120.00251.04 0.21525 18409.6 1 2 3 5 120.00334.72 0.24162 29288.0 1 2 385 5 120.00334.72 0.24162 29288.0 3 2 385 5 120.00334.72 0.24162 29288.0 2 3 4 5
Re: [gmx-users] energy minimization problem
Hi Justin, the snapshot I uploaded in the URL is of the SSDNA-CNT system after energy minimization step not before it. I stripped off water and ions from the system for the ease of visualization. I would be grateful if you suggest me a possible way out. Regards, Soumadwip Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Thanks Justin for your quick reply. What are the correct non-bonding settings for CHARMM to be used in the .mdp file? Here is how the CNT molecule looks like prior to energy minimization. pre energy min CNT https://drive.google.com/file/d/0B7SBnQ5YXQSLX0dIOHZjT3p1Y2s/view?usp=sharing I am not continuing any of the equilibration steps anymore. As you can see the CNT structure is distorted badly. Please help me out. What settings do I need to change in order to avoid such distortion? Is there a possibility that the cnt topology was wrong to begin with? Regards, Soumadwip Research Fellow IITB India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization problem
Hi Tsjerk, My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro I downloaded the CG water model from martini protein tutorial website. Is there anything wrong? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe
Re: [gmx-users] energy minimization problem
Hi Tsjerk, I used the original structure generated by sabbac. My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro I downloaded the CG water model from martini protein tutorial website. Is there anything wrong? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http
Re: [gmx-users] energy minimization problem
Besides, the martini.itp does not contain moleculetype CL, so I edit it like this: [ moleculetype ] ; molname nrexcl CL1 [ atoms ] ;id typeresnr residu atomcgnrcharge 1 P4 1 CL CL 1 -1 Please help to have a look. I do not know whether it is true or not, as the small triple helix used for test does not carry charge, so I did not add CL. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang Sent: Monday, 18 May 2015 7:04 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem Hi Tsjerk, I used the original structure generated by sabbac. My computer has 8 cores only, martini simulation looks much faster than full atomic simulation. The command I used is here: python martinize.py -f hyp.pdb -o system-vaccum.top -x hyp-CG.pdb -ss hyp_lys -p backbone -ff martini22 -collagen editconf -f hyp-CG.pdb -c -d 1 -o hyp-CG-box.pdb grompp -f minimization-vaccum.mdp -p system-vaccum.top -c hyp-CG-box.pdb -o minimization-vaccum.tpr mdrun -deffnm minimization-vaccum -v gmx solvate -cp minimization-vaccum.gro -cs water-box-CG_303K-1bar.gro -radius 0.21 -o system-solvated.gro I downloaded the CG water model from martini protein tutorial website. Is there anything wrong? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing the original structure, or did you use the relaxed structure from the atomistic simulation? How did you solvate the system? Cheers, Tsjerk On May 18, 2015 10:29, Ming Tang m21.t...@qut.edu.au wrote: Hi Tsjerk, I just tried, but it stopped for too many LICS warnings at step 6000. Small triple helix can be equilibrated for 1000ns with NPT. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation
Re: [gmx-users] energy minimization problem
Hi Tsjerk, This protein has a total charge of 35e, and I added 35 CL to balance the system. Is there any difference between adding CL and not adding CL? Thank you. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t...@qut.edu.au wrote: Thanks a lot, Justin It really makes me feel weird. The small triple helix with 30 amino acids per chain(generated simply by deleting other atoms in .pdb file of the real triple helix) can be equilibrated for 1ns using exactly the same control files, and the real triple helix can be used for full atomic simulation without any problem. The CG topology is generated using the same mitinize.py downloaded from the website. I will try for another time, and will tell you if I fix it. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step. Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe. This seems entirely random and suggests instead that there is something simply physically unstable with the system or problematic in the topology. I don't use MARTINI (or CG models in general) so there's little else I can suggest. Maybe someone more experienced with such systems will chime in. Also note that a chain moving into another box is probably just a PBC effect and not a true dissociation. If it is a dissociation, it's not simply because of the time step. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
On 5/16/15 11:35 PM, James Lord wrote: Hi Justin Thanks for this. Can you tell me which step(s) this bond length is defined What should I do (redo) to resolve this issue? The bonds are defined in the topology. The DD algorithm reads what's in the coordinate file and builds cells based on the geometry it finds there. Without a full description of what's in your system, what steps you've taken to prepare it (full commands, in order), there's little I can suggest because it would all be guesswork. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization error
On 5/16/15 6:27 AM, James Lord wrote: Dear gmx users, I am getting this error, Can anyone help me to get around this? Cheers James Program mdrun, VERSION 4.6.3 Source code file: /home/james/gromacs-4.6.3/src/mdlib/domdec.c, line: 6792 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.93203 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition Log file opened on Sat May 16 22:15:44 2015 Host: james-E530 pid: 22300 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6.3 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: AVX_256 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Wed Oct 30 18:28:46 NZDT 2013 Built by: james@james-E530 [CMAKE] Build OS/arch: Linux 3.11.0-12-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz Build CPU family: 6 Model: 58 Stepping: 9 Build CPU features: apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.8.1-10ubuntu8) 4.8.1 C compiler flags: -mavx-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = steep nsteps = 5 init-step= 0 cutoff-scheme= Group ns_type = Grid nstlist = 5 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 56 nky = 56 nkz = 144 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface
Re: [gmx-users] energy minimization problem
On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
On 5/15/15 9:32 AM, Ming Tang wrote: Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps The time step will depend on the stability of the system, which in turn depends on how well equilibrated it is. If reducing the time step promotes stability during equilibration, that is the most obvious solution. After equilibrating for a while, try increasing the time step. -Justin Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you. define = -DPOSRES integrator = md dt = 0.02 Have you tried simply reducing the time step? 20 fs may be reasonable for a well equilibrated system, but if the run is dying early, then this is the first thing I would look at. -Justin nsteps = 5 nstxout = 0 nstvout = 0 nstlog = 1000 nstxtcout= 1000 xtc-precision= 10 cutoff-scheme=verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.9 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = force-switch rvdw-switch = 0.9 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein W tau-t= 1.0 1.0 ref-t= 310 310 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 11:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
Dear Justin, could you please tell me how to get the maximum force of an exact atom? I tried g_traj -of, but did not get any force data. Thanks a lot. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 2:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 3:12 AM, Ming Tang wrote: Dear all, I am working with a triple helix containing around 1000 amino acids per chain using martini force field. After energy minimization until it cannot be minimized any more, I moved to NPT, but got LINCS error after thousands of steps. Following Justin's advice on LINCS error, I checked all of the possible causes in blowing up page, but still did not find the reason. Later, I created a smaller model including 30 amino acids per chain, and found it could be move forward to dynamic simulation smoothly using the same control files. Does this mean that my control files are ok? I noticed that the minimization was not good enough when working with my real triple helix, as it got stuck in a certain atom (Epot does not change). I have tried to change to use cg algorithm, but got no improvement. Could anybody tell me how to further minimize my triple helix. I got stuck here for 3 days. Sounds like your initial geometry is just bad. Inspect the surroundings of the atom with maximum force; that usually gives an indication of what's going on. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization problem
On 5/14/15 9:47 PM, Ming Tang wrote: Dear Justin, I saw it in the terminal. Potential Energy = -6.3682131e+05 Maximum force = 1.8876091e+02 on atom 1147 Norm of force = 3.1155257e+00 But, how can I further minimize my protein? Minimization is not your problem. Post a full .mdp file of the run that is failing. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.