[gmx-users] Energy minimization has stopped....
Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: The Feeling of Power was Intoxicating, Magic (Frida Hyvonen) -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization has stopped....
What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching the Fmax cutoff. 2 is a large number of steps. Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: The Feeling of Power was Intoxicating, Magic (Frida Hyvonen) -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization has stopped....
On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization has stopped....
Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization has stopped....
On 11/5/13 7:31 AM, Kalyanashis Jana wrote: Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. You should first do what I suggested before. The reason for a large force is either (1) bad atomic clashes that should be apparent upon visual inspection or (2) bad topology for the drug. -Justin On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization problem
On 11/3/13 6:20 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtolshould be lower than 1. As I understand, you mean that for these systems emtol should be 0 or negative. Is it really true? No. You are not likely to ever achieve zero force, and a negative value is impossible. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] energy minimization problem
Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10. I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful? Best Regards Kiana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization problem
On 11/2/13 3:38 PM, kiana moghaddam wrote: Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10. I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful? The purpose of EM is to generate a reasonable configuration that can be subjected to dynamics. For most standard MD, an emtol in the neighborhood of 100-1000 is sufficient, and there are no hard and fast rules that I know of that motivates that choice. If MD fails, run EM again with a lower tolerance. For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and in double precision. As long as the potential energy is negative and in a range that is expected given the size of the system (10^5 - 10^6 in the case of most solvated proteins or membranes), the outcome is probably acceptable. The number of steps is largely irrelevant; the energetic outcome is far more important. I usually set nsteps to some huge value and just let EM converge as far as it will. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] energy minimization
Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. I would like to know how to solve these problems? best regards -- *Marzieh Dehghan PhD Candidate of Biochemistry Institute of biochemistry and Biophysics (IBB) University of Tehran, Tehran- Iran.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization
On 9/23/13 3:08 AM, marzieh dehghan wrote: Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. Chain IDs are irrelevant in Gromacs, but can be restored by converting file formats using trjconv and a .tpr file. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. This may or may not be a simple PBC effect (again, fixed with trjconv). If the bond exists in the topology, it cannot be broken. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization
On Sep 23, 2013 9:08 AM, marzieh dehghan dehghanmarz...@gmail.com wrote: Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. Did pdb2gmx even report it being made? Mark I would like to know how to solve these problems? best regards -- *Marzieh Dehghan PhD Candidate of Biochemistry Institute of biochemistry and Biophysics (IBB) University of Tehran, Tehran- Iran.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization failure
Greetings, I am relatively new to MD, and I am attempting to simulate a metal-organic framework but I don't seem to be even able to get past the energy minimization phase. I could appreciate any insight into what I might be doing wrong. Here is a brief summary of what I have done: - constructed a PDB file from the crystal structure coordinates of a model compound, capping the organic linker with phenyl and capping the metal atoms with water and hydroxide ions to yield a full coordination sphere and to yield a net charge of zero - constructed a custom force field using published parameters - run pdb2gmx to construct the .gro and .top files - run editconf to construct a box around the MOF, 5 nm in each dimension - run genbox to fill the box with water - run grompp to prepare the box for addition of ions - run genion to replace 20 solvent molecules with 10 Na+ and 10 Cl- ions - manually edit the topology file (per the suggestion here on the listserv of a few days ago) to include, in the [ pairs ] directive, all pair interactions for purposes of electrostatic computation, but with parameters of 0 0 for the van der Waals parameters, so as to have the van der Waals interactions remain the usual case of neglected for 1-2 and 1-3 interactions - create an index file containing a group that has the 60 atoms constituting the terminal water and hydroxide ion atoms, so as to keep their coordinates frozen during the minimization - run grompp again to prepare the box for energy minimization (below is the minim.mdp file used for this) - run mdrun to perform the energy minimization The energy minimization does not yield the maximum force falling below the desired 1000, but stays as high as 10^6. Visualization of the output .gro file yields that many atoms within the core of the MOF have moved into strange positions, i.e., the formation of seeming O-O bonds between adjacent carboxylates when instead both O atoms should be coordinated to the metal atom. The calculations yielded a great deal of data, and so as not to clog everybody's inboxes, I only included the one that seemed most relevant (minim.mdp). If there is something else required, I'll happily share it. I am not sure what's going on and I could appreciate any insight into what might be causing this and how to fix it. Thanks in advance , Jeff Woodford Assistant Professor of Chemistry Missouri Western State University minim.mdp: ; 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 = 1.5 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.5 ; Short-range electrostatic cut-off rvdw = 1.5 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) freezegrps = Terminal_atoms freezedim = Y Y Y -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization failure
On Tue, Mar 19, 2013 at 9:16 AM, Jeff Woodford jwoodf...@missouriwestern.edu wrote: Greetings, I am relatively new to MD, and I am attempting to simulate a metal-organic framework but I don't seem to be even able to get past the energy minimization phase. I could appreciate any insight into what I might be doing wrong. Here is a brief summary of what I have done: - constructed a PDB file from the crystal structure coordinates of a model compound, capping the organic linker with phenyl and capping the metal atoms with water and hydroxide ions to yield a full coordination sphere and to yield a net charge of zero - constructed a custom force field using published parameters - run pdb2gmx to construct the .gro and .top files - run editconf to construct a box around the MOF, 5 nm in each dimension - run genbox to fill the box with water - run grompp to prepare the box for addition of ions - run genion to replace 20 solvent molecules with 10 Na+ and 10 Cl- ions - manually edit the topology file (per the suggestion here on the listserv of a few days ago) to include, in the [ pairs ] directive, all pair interactions for purposes of electrostatic computation, but with parameters of 0 0 for the van der Waals parameters, so as to have the van der Waals interactions remain the usual case of neglected for 1-2 and 1-3 interactions - create an index file containing a group that has the 60 atoms constituting the terminal water and hydroxide ion atoms, so as to keep their coordinates frozen during the minimization - run grompp again to prepare the box for energy minimization (below is the minim.mdp file used for this) - run mdrun to perform the energy minimization The energy minimization does not yield the maximum force falling below the desired 1000, but stays as high as 10^6. Visualization of the output .gro file yields that many atoms within the core of the MOF have moved into strange positions, i.e., the formation of seeming O-O bonds between adjacent carboxylates when instead both O atoms should be coordinated to the metal atom. The calculations yielded a great deal of data, and so as not to clog everybody's inboxes, I only included the one that seemed most relevant (minim.mdp). If there is something else required, I'll happily share it. I am not sure what's going on and I could appreciate any insight into what might be causing this and how to fix it. I would suggest a few things: 1. Simplify as much as possible, using small units of structure to diagnose. 2. Look at various energy terms in the .edr file. One will likely stick out like a sore thumb in terms of being huge and positive, hence the large forces. My suspicion would be short-range Coulombic forces. Including nonbonded terms in 1-2 and 1-3 interactions is very weird, since they may oppose the normal bonded forces. The bonds you see forming are not actually there. Your visualization program is just guessing what's going on. It's certainly indicative of bad geometry, but no bonds are breaking or forming, unless you're doing QM and not telling us ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy Minimization/ NpT settling problem
Hi, I am trying to simulate a system consisting of 1790 molecules of monoethanolamine (MEA), 203 molecules of CO2 and 18210 molecules of water. After having generated my box and set the density to 1000g/l using editconf, I am facing a problem with the energy minimization step. It does not converge to the tolerence I give (Fmax500kJ/mol). I get this message: Steepest Descents converged to machine precision in 199 steps, but did not reach the requested Fmax 500. Potential Energy = -9.27407663461033e+05 Maximum force = 2.07667591793109e+06 on atom 13090 Norm of force = 1.06912622245517e+04 Since no problem occurs when I simulate CO2 with water only, I think the problem comes from MEA for which I apply an OPLS_AA force field. I tried lots of different initial configurations for MEA, using structures developed with the Avogadro program and structures from data bank found on the net. All of them result in the same convergence problem. I don't think there is an issue in my mdp file as I use it for other simulations which work well. It is as follow: 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 = 500.0 ; Stop minimization when the maximum force 500.0 kJ/mol emstep = 0.001 ; Energy step size nsteps = 10; 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 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) I also tried another approach: I inserted the molecules in a much more bigger box and performed the energy minimization of this system with a very low density. This could converge. Afterwards, I run an npT simulation with a high pressure (10 bar) such that the box shrinks and that the system reachs the good density. At that step, the following error came out: Making 1D domain decomposition 12 x 1 x 1 starting mdrun 'CO2 in MEA at 303K' 5000 steps, 5.0 ps. ^Mstep 0imb F 4% ^Mstep 100, remaining runtime: 132 s step 134: Water molecule starting at atom 24060 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates --- Program mdrun_d, VERSION 4.5.5 Source code file: pme.c, line: 538 Fatal error: 1 particles communicated to PME node 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can someone tell me where I am making any mistake and why is my system not converging? Thanks in advance, Emmanuelle MSc student -TU Delft -- View this message in context: http://gromacs.5086.n6.nabble.com/Energy-Minimization-NpT-settling-problem-tp5003976.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Energy Minimization/ NpT settling problem
A couple of things: 1. Are your cutoffs appropriate for OPLS_AA? Even if you fix any code problems and using the wrong cutoffs, your results will not be meaningful... 2. How are you generating your box/filling it with molecules? There are indications that your original box is too small, or that there are clashing atoms in the original configuration, since with a much bigger box you don't seem to have problems except for particles moving too rapidly for domain decomposition to handle (perhaps there is a cutoff/coupling problem). 2b: what is atom 13090 and what is in its vicinity? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of emmanuelle [e.a.y.m...@student.tudelft.nl] Sent: Thursday, December 20, 2012 2:31 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy Minimization/ NpT settling problem Hi, I am trying to simulate a system consisting of 1790 molecules of monoethanolamine (MEA), 203 molecules of CO2 and 18210 molecules of water. After having generated my box and set the density to 1000g/l using editconf, I am facing a problem with the energy minimization step. It does not converge to the tolerence I give (Fmax500kJ/mol). I get this message: Steepest Descents converged to machine precision in 199 steps, but did not reach the requested Fmax 500. Potential Energy = -9.27407663461033e+05 Maximum force = 2.07667591793109e+06 on atom 13090 Norm of force = 1.06912622245517e+04 Since no problem occurs when I simulate CO2 with water only, I think the problem comes from MEA for which I apply an OPLS_AA force field. I tried lots of different initial configurations for MEA, using structures developed with the Avogadro program and structures from data bank found on the net. All of them result in the same convergence problem. I don't think there is an issue in my mdp file as I use it for other simulations which work well. It is as follow: 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 = 500.0 ; Stop minimization when the maximum force 500.0 kJ/mol emstep = 0.001 ; Energy step size nsteps = 10; 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 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) I also tried another approach: I inserted the molecules in a much more bigger box and performed the energy minimization of this system with a very low density. This could converge. Afterwards, I run an npT simulation with a high pressure (10 bar) such that the box shrinks and that the system reachs the good density. At that step, the following error came out: Making 1D domain decomposition 12 x 1 x 1 starting mdrun 'CO2 in MEA at 303K' 5000 steps, 5.0 ps. ^Mstep 0imb F 4% ^Mstep 100, remaining runtime: 132 s step 134: Water molecule starting at atom 24060 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates --- Program mdrun_d, VERSION 4.5.5 Source code file: pme.c, line: 538 Fatal error: 1 particles communicated to PME node 7 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Can someone tell me where I am making any mistake and why is my system not converging? Thanks in advance, Emmanuelle MSc student -TU Delft -- View this message in context: http://gromacs.5086.n6.nabble.com/Energy-Minimization-NpT-settling-problem-tp5003976.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
Read through the log file to find out what atoms are causing the system to crash. I also prefer running mdrun -v and capturing that too, since it provides similar log data but does not output the energy tables. You also did not specify what the final maximum forces were in the system after the last round of minimization or what atom had the highest force at the end of the EM. If you did anything weird with the protein, you may have to go through the entire structure sidechain by sidechain to make sure that there are no weird connectivities (Once I had a peptide bond from a coil going straight through the plane of a benzene ring in a far-away residue, and the simulation would always crash because the forces of the covalent bonds in the ring would blow up as it clashed with the forces calculated for the peptide bond and this was not noticed during minimization). On 2012-12-17 03:04:47AM -0800, Shima Arasteh wrote: Dears, I changed the coordinates of overlapping atoms and got a normal potential energy. Then when I go to the next step ( NVT equilibrium ), it doesn't run and I just get some pdb files. How is it possible to find the problem? It might be clashes in the system but How can I find the overlapping atoms and the reason of clashe among a vast number of atoms? Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, December 16, 2012 11:18 AM Subject: Re: [gmx-users] Energy minimization Probably remove the overlapping lipid then. Once you run MD it will repack. On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote: Thanks for your kind reply. My system is composed of protein packed by lipids. The atoms overlapping, are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, December 16, 2012 8:44 AM Subject: Re: [gmx-users] Energy minimization It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem
Re: [gmx-users] Energy minimization
Dears, I changed the coordinates of overlapping atoms and got a normal potential energy. Then when I go to the next step ( NVT equilibrium ), it doesn't run and I just get some pdb files. How is it possible to find the problem? It might be clashes in the system but How can I find the overlapping atoms and the reason of clashe among a vast number of atoms? Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, December 16, 2012 11:18 AM Subject: Re: [gmx-users] Energy minimization Probably remove the overlapping lipid then. Once you run MD it will repack. On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote: Thanks for your kind reply. My system is composed of protein packed by lipids. The atoms overlapping, are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, December 16, 2012 8:44 AM Subject: Re: [gmx-users] Energy minimization It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org
Fw: [gmx-users] Energy minimization
Sincerely, Shima - Forwarded Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Dariush Mohammadyani d.mohammady...@gmail.com Sent: Sunday, December 16, 2012 5:03 PM Subject: Re: [gmx-users] Energy minimization It's printed in terminal, exactly before showing the values of infinite potential and Max Force and . Sincerely, Shima From: Dariush Mohammadyani d.mohammady...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, December 16, 2012 5:01 PM Subject: Re: [gmx-users] Energy minimization Hi Shima, Just for my knowledge, how did you find the clashed atom? Thanks, Dariush On Sun, Dec 16, 2012 at 12:19 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. -- Dariush Mohammadyani Ph.D Student Department of Bioengineering University of Pittsburgh Pittsburgh, USA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
It's printed in terminal, exactly before showing the values of infinite potential and Max Force and . Sincerely, Shima From: Dariush Mohammadyani d.mohammady...@gmail.com To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Sunday, December 16, 2012 5:01 PM Subject: Re: [gmx-users] Energy minimization Hi Shima, Just for my knowledge, how did you find the clashed atom? Thanks, Dariush On Sun, Dec 16, 2012 at 12:19 AM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. -- Dariush Mohammadyani Ph.D Student Department of Bioengineering University of Pittsburgh Pittsburgh, USA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
Thanks for your kind reply. My system is composed of protein packed by lipids. The atoms overlapping, are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, December 16, 2012 8:44 AM Subject: Re: [gmx-users] Energy minimization It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
Probably remove the overlapping lipid then. Once you run MD it will repack. On 2012-12-15 09:19:49PM -0800, Shima Arasteh wrote: Thanks for your kind reply. My system is composed of protein packed by lipids. The atoms overlapping, are protein ( atom 288) and lipid chain. I think if I move them, I may get some other clashes, may I not? Any other suggestion? Thanks. Sincerely, Shima - Original Message - From: Peter C. Lai p...@uab.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Sunday, December 16, 2012 8:44 AM Subject: Re: [gmx-users] Energy minimization It depends on what the atom is overlapping with and some conjecture as to what might be causing the overlap: You can always manually move it, either by editing the .gro file directly or using a tool like VMD to move it or the molecule/fragment it's attached to with the mouse and then display the new coordinates and the update the .gro file. If it's something like a solvent molecule (water/lipid) and there is nowhere to move the molecule, you can try deleting it too (just remmeber to update .top file). On 2012-12-15 08:58:59PM -0800, Shima Arasteh wrote: When I find overlapping atom, what should I have to do? How is it possible to get solved? Would you please help me? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, September 29, 2012 3:01 PM Subject: Re: [gmx-users] Energy minimization On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization with walls
Hi all, I am simulating a box filled only with water and having walls at Z=0 and Z=Z_box. I am confused that whether energy minimization process removes the bad contacts between wall atoms and solvent or not ? any kind of help would be really appreciated -- View this message in context: http://gromacs.5086.n6.nabble.com/Energy-minimization-with-walls-tp5003229.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization
Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Thanks in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
On 9/29/12 3:19 AM, Shima Arasteh wrote: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force =inf on atom 518 Norm of force =inf It seems that atome 518 has an infinite energy. So I tried to apply the suggestion of turning off the constraints in em.mdp. To do so, I added constraints=none to mdp file, But it doesn't make different. Any suggestion please? I don't know how to solve this problem. Please help me. Atom 518 is overlapping with something nearby. You will have to visualize the system to identify the source of the problem. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] energy minimization output
Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force = inf on atom 518 Norm of force = inf Why the maximum force and norm of it is not written? I repeated it for a few times, but no difference. Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization output
26 sep 2012 kl. 08.16 skrev Shima Arasteh: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force =inf on atom 518 Norm of force =inf Why the maximum force and norm of it is not written? I repeated it for a few times, but no difference. It's written. Unfortunately it's infinite. Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization output
Dear Erik, I also encountered similar problem. So you mean it cannot be further energy minimized? How can we proceed with NPT if the system is not in equilibrium? On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 26 sep 2012 kl. 08.16 skrev Shima Arasteh: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force =inf on atom 518 Norm of force =inf Why the maximum force and norm of it is not written? I repeated it for a few times, but no difference. It's written. Unfortunately it's infinite. Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization output
It seems that your input structure has too severe clashes for energy minimization, that there are problems with your topology, or that your mdp options are not adequate. One possible solution, if your topology is correct, is to first perform an energy minimization using soft-core potentials to get rid of some of the structural strain. In any case you should inspect your structure closely, in particular near atom 518. Erik 26 sep 2012 kl. 10.23 skrev Archana Sonawani: Dear Erik, I also encountered similar problem. So you mean it cannot be further energy minimized? How can we proceed with NPT if the system is not in equilibrium? On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 26 sep 2012 kl. 08.16 skrev Shima Arasteh: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr and then: # mdrun -v -deffnm em The output is: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 2.30004e+17 Fmax= inf, atom= 518 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.3# Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 2.3000388e+17 Maximum force =inf on atom 518 Norm of force =inf Why the maximum force and norm of it is not written? I repeated it for a few times, but no difference. It's written. Unfortunately it's infinite. Thanks for your suggestions in advance. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy Minimization of Alanin
Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.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 Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization of Alanin
On 9/19/12 6:04 AM, Lara Bunte wrote: Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps= 5000 nstlist = 1 rlist= 0.7 coulombtype = PME rcoulomb= 0.7 vdw-type= cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.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 Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. For EM, the balance of PME vs PP interactions does not matter so much, so you don't necessarily need to take action for this reason. If you are using CHARMM27, however, your cutoffs are completely wrong so you should correct them to have a sensible trajectory. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization of Alanin
for EM you can probably ignore this, but note that these are the wrong cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch). On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote: Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.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 Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization of Alanin
Hi Thanks for the help. I changed this cut-off parameters and increased the distance between my box und the solute from 0.5 to 1.5. I got no error and no note. :-) Greetings Lara - Ursprüngliche Message - Von: Peter C. Lai p...@uab.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 12:12 Mittwoch, 19.September 2012 Betreff: Re: [gmx-users] Energy Minimization of Alanin for EM you can probably ignore this, but note that these are the wrong cutoffs for CHARMM27. (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch). On 2012-09-19 11:04:47AM +0100, Lara Bunte wrote: Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this box. With genbox and the solvation I used spc216 model. Next I want to run an energy minimization and I create this em.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 5000 nstlist = 1 rlist = 0.7 coulombtype = PME rcoulomb = 0.7 vdw-type = cut-off rvdw = 0.7 nstenergy = 10 grompp works but I got this note: NOTE 1 [file em.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 Is this necessary for me to increase cut-off and PME grid spacing or can I ignore this note? I would be thankful if you could explain that to me. Thanks for help Greetings Lara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy Minimization - not getting correct lipid area
Hi, I am working through the KALP-15 tutorial and having difficulties getting the correct area per lipid (~71 A^2). I first scaled the lipid by a factor of 4 (perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) then did energy minimization (mdrun -v -deffnm em) and then scaled down by 0.95 (perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink.gro 5 area_shrink1.dat). The tutorial then said to do energy minimizations and scale by 0.95 until the correct area per lipid is reached. When I do, my numbers stay the same, i.e. all three are 0.583197761890625 nm^2. Any suggestions? Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization - not getting correct lipid area
On 6/8/12 3:15 PM, Hicks, Erica wrote: Hi, I am working through the KALP-15 tutorial and having difficulties getting the correct area per lipid (~71 A^2). I first scaled the lipid by a factor of 4 (perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) then did energy minimization (mdrun -v -deffnm em) and then scaled down by 0.95 (perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink.gro 5 area_shrink1.dat). The tutorial then said to do energy minimizations and scale by 0.95 until the correct area per lipid is reached. When I do, my numbers stay the same, i.e. all three are 0.583197761890625 nm^2. Any suggestions? After how many iterations? If you've hit 0.58 nm^2, you've gone too far. You'll likely hit a point where you can't squeeze the lipids any more, but 25-26 iterations consistently gives the value stated in the tutorial. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization of crystal structure with water
On 18/03/2012 1:01 PM, NG HUI WEN wrote: Hi all, I have a seemingly simple task that turned quite tricky here. I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS). The problem I am facing now is that after energy minimization, the protein and water (originally in the protein cavity) were found in completely different coordinate space. Using pbc box in VMD, I found that the water was found roughly at the original space but not the protein. I have tried (all turned out futile) 1) EM with and without pbc 2) position restraint the protein backbone and water Would someone be able to help me on this? I know I must have done something silly here. This is normal. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Energy minimization of crystal structure with water
Hi Mark, Thanks - I completely forgot about that! Cheers, Huiwen From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Sunday, March 18, 2012 2:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization of crystal structure with water On 18/03/2012 1:01 PM, NG HUI WEN wrote: Hi all, I have a seemingly simple task that turned quite tricky here. I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS). The problem I am facing now is that after energy minimization, the protein and water (originally in the protein cavity) were found in completely different coordinate space. Using pbc box in VMD, I found that the water was found roughly at the original space but not the protein. I have tried (all turned out futile) 1) EM with and without pbc 2) position restraint the protein backbone and water Would someone be able to help me on this? I know I must have done something silly here. This is normal. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization of crystal structure with water
Hi all, I have a seemingly simple task that turned quite tricky here. I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS). The problem I am facing now is that after energy minimization, the protein and water (originally in the protein cavity) were found in completely different coordinate space. Using pbc box in VMD, I found that the water was found roughly at the original space but not the protein. I have tried (all turned out futile) 1) EM with and without pbc 2) position restraint the protein backbone and water Would someone be able to help me on this? I know I must have done something silly here. Thank you. Huiwen This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK Malaysia legislation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization Error
I achieve Steepest Descents converged to machine precision in 205 steps, but did not reach the requested Fmax 10. Potential Energy = -1.49131940478719e+07 Maximum force = 1.09664530279637e+06 on atom 1520(parto of the protein) Norm of force = 2.28369808518165e+06 and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there might have been an error in the way I defined the position restraints, in fact in the mdp file I hade define = -DEPOSRE while in the topology I had ifdef DEFINE_WAT, so it might have moved it all without fixing the water. So I tried again and this time I got Steepest Descents converged to machine precision in 72 steps, but did not reach the requested Fmax 10. Potential Energy = -2.0135496e+07 Maximum force = 2.0486184e+12 on atom 4479 Norm of force = 7.2424045e+13 but again the same issue with table extent and still the production of pdb files. Any explanations? Thanks Francesca 2012/2/9 Justin A. Lemkul jalem...@vt.edu francesca vitalini wrote: Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? What is the Fmax you achieve, and what are your intents for this process? Minimizing very low is only strictly necessary for certain types of very sensitive calculations. For normal MD, convergence below 100-1000 kJ/mol-nm is typical. Other algorithms are listed in the manual. They may or may not be necessary. -Justin 2012/2/9 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. 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_**precisionhttp://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 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_precisionhttp://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 Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps
Re: [gmx-users] Energy minimization Error
francesca vitalini wrote: I achieve Steepest Descents converged to machine precision in 205 steps, but did not reach the requested Fmax 10. Potential Energy = -1.49131940478719e+07 Maximum force = 1.09664530279637e+06 on atom 1520(parto of the protein) Norm of force = 2.28369808518165e+06 The magnitude of the force suggests atomic overlap somewhere. Start by investigating the environment around atom 1520. and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there The step.pdb files are written when mdrun is about to crash. might have been an error in the way I defined the position restraints, in fact in the mdp file I hade define = -DEPOSRE while in the topology I had ifdef DEFINE_WAT, so it might have moved it all without fixing the water. So I tried again and this time I got The define statements are literal, so be careful of typos. -DEPOSRE will not work when the topology calls for -DPOSRES. So unless you've changed default naming for define statements, you're not going to get what you expect. Steepest Descents converged to machine precision in 72 steps, but did not reach the requested Fmax 10. Potential Energy = -2.0135496e+07 Maximum force = 2.0486184e+12 on atom 4479 Norm of force = 7.2424045e+13 Again, symptomatic of severe atomic overlap. but again the same issue with table extent and still the production of pdb files. Any explanations? Investigate the starting configurations near the problematic atoms. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization Error
In order to overcome the problem I tried to fix everything except the backbone (solvent, sidechain and CA, as I want the structure to be maintained). However, if I do then I have problems with the energy minimization as the force on the 15300 is infinite. Getting Loaded... Reading file EM1-1.tpr, VERSION 3.3.1 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 ---inf, atom= 15300 Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 27744 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Oh My God ! It's the Funky Shit (Beastie Boys) Halting program mdrun You suggested to check if there is any overlapping. There might be as my structure is obtained through a reverse transformation from a CG representation. In the mapping the atoms are positioned randomly in the bead. Now I'm running some energy minimization to equilibrate those atoms. I had to solvate the system after the mapping (couldn't do it before due to problems with ions)but I haven't equilibrated it yet and I'm keeping it fixed which could also be a source of overlapping. Any ideas? Thanks. Francesca 2012/2/10 Justin A. Lemkul jalem...@vt.edu francesca vitalini wrote: I achieve Steepest Descents converged to machine precision in 205 steps, but did not reach the requested Fmax 10. Potential Energy = -1.49131940478719e+07 Maximum force = 1.09664530279637e+06 on atom 1520(parto of the protein) Norm of force = 2.28369808518165e+06 The magnitude of the force suggests atomic overlap somewhere. Start by investigating the environment around atom 1520. and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there The step.pdb files are written when mdrun is about to crash. might have been an error in the way I defined the position restraints, in fact in the mdp file I hade define = -DEPOSRE while in the topology I had ifdef DEFINE_WAT, so it might have moved it all without fixing the water. So I tried again and this time I got The define statements are literal, so be careful of typos. -DEPOSRE will not work when the topology calls for -DPOSRES. So unless you've changed default naming for define statements, you're not going to get what you expect. Steepest Descents converged to machine precision in 72 steps, but did not reach the requested Fmax 10. Potential Energy = -2.0135496e+07 Maximum force = 2.0486184e+12 on atom 4479 Norm of force = 7.2424045e+13 Again, symptomatic of severe atomic overlap. but again the same issue with table extent and still the production of pdb files. Any explanations? Investigate the starting configurations near the problematic atoms. http://www.gromacs.org/**Documentation/Terminology/** Blowing_Up#Diagnosing_an_**Unstable_Systemhttp://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 --
Re: [gmx-users] Energy minimization Error
On 11/02/2012 12:41 AM, francesca vitalini wrote: In order to overcome the problem I tried to fix everything except the backbone (solvent, sidechain and CA, as I want the structure to be maintained). However, if I do then I have problems with the energy minimization as the force on the 15300 is infinite. Getting Loaded... Reading file EM1-1.tpr, VERSION 3.3.1 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 ---inf, atom= 15300 Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 27744 ] Please report this to the mailing list (gmx-users@gromacs.org mailto:gmx-users@gromacs.org) --- Oh My God ! It's the Funky Shit (Beastie Boys) Halting program mdrun You suggested to check if there is any overlapping. ... so you need to get out some visualization software and look at the transformed structure :) There might be as my structure is obtained through a reverse transformation from a CG representation. In the mapping the atoms are positioned randomly in the bead. Now I'm running some energy minimization to equilibrate those atoms. I had to solvate the system after the mapping (couldn't do it before due to problems with ions)but I haven't equilibrated it yet and I'm keeping it fixed which could also be a source of overlapping. Local minimization with EM cannot in general take a random positioning of the generated atoms and make it one that will be stable under MD. Some structure knowledge needs to be build into the reverse transformation. Mark Any ideas? Thanks. Francesca 2012/2/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu francesca vitalini wrote: I achieve Steepest Descents converged to machine precision in 205 steps, but did not reach the requested Fmax 10. Potential Energy = -1.49131940478719e+07 Maximum force = 1.09664530279637e+06 on atom 1520 (parto of the protein) Norm of force = 2.28369808518165e+06 The magnitude of the force suggests atomic overlap somewhere. Start by investigating the environment around atom 1520. and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there The step.pdb files are written when mdrun is about to crash. might have been an error in the way I defined the position restraints, in fact in the mdp file I hade define = -DEPOSRE while in the topology I had ifdef DEFINE_WAT, so it might have moved it all without fixing the water. So I tried again and this time I got The define statements are literal, so be careful of typos. -DEPOSRE will not work when the topology calls for -DPOSRES. So unless you've changed default naming for define statements, you're not going to get what you expect. Steepest Descents converged to machine precision in 72 steps, but did not reach the requested Fmax 10. Potential Energy = -2.0135496e+07 Maximum force = 2.0486184e+12 on atom 4479 Norm of force = 7.2424045e+13 Again, symptomatic of severe atomic overlap. but again the same issue with table extent and still the production of pdb files. Any explanations? Investigate the starting configurations near the problematic atoms. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] Energy minimization Error
In fact in the reverse transformation I'm feeding the CG structure information. Once I look through VMD to the FG structure I notice that the backbones are not in planes so definitely I need to run some minimization there. In the tutorial they were using simulating annealing, but I don't think I need more than energy minimization for that. What do you think? 2012/2/10 Mark Abraham mark.abra...@anu.edu.au On 11/02/2012 12:41 AM, francesca vitalini wrote: In order to overcome the problem I tried to fix everything except the backbone (solvent, sidechain and CA, as I want the structure to be maintained). However, if I do then I have problems with the energy minimization as the force on the 15300 is infinite. Getting Loaded... Reading file EM1-1.tpr, VERSION 3.3.1 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 ---inf, atom= 15300 Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 27744 ] Please report this to the mailing list (gmx-users@gromacs.org) --- Oh My God ! It's the Funky Shit (Beastie Boys) Halting program mdrun You suggested to check if there is any overlapping. ... so you need to get out some visualization software and look at the transformed structure :) There might be as my structure is obtained through a reverse transformation from a CG representation. In the mapping the atoms are positioned randomly in the bead. Now I'm running some energy minimization to equilibrate those atoms. I had to solvate the system after the mapping (couldn't do it before due to problems with ions)but I haven't equilibrated it yet and I'm keeping it fixed which could also be a source of overlapping. Local minimization with EM cannot in general take a random positioning of the generated atoms and make it one that will be stable under MD. Some structure knowledge needs to be build into the reverse transformation. Mark Any ideas? Thanks. Francesca 2012/2/10 Justin A. Lemkul jalem...@vt.edu francesca vitalini wrote: I achieve Steepest Descents converged to machine precision in 205 steps, but did not reach the requested Fmax 10. Potential Energy = -1.49131940478719e+07 Maximum force = 1.09664530279637e+06 on atom 1520(parto of the protein) Norm of force = 2.28369808518165e+06 The magnitude of the force suggests atomic overlap somewhere. Start by investigating the environment around atom 1520. and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there The step.pdb files are written when mdrun is about to crash. might have been an error in the way I defined the position restraints, in fact in the mdp file I hade define = -DEPOSRE while in the topology I had ifdef DEFINE_WAT, so it might have moved it all without fixing the water. So I tried again and this time I got The define statements are literal, so be careful of typos. -DEPOSRE will not work when the topology calls for -DPOSRES. So unless you've changed default naming for define statements, you're not going to get what you expect. Steepest Descents converged to machine precision in 72 steps, but did not reach the requested Fmax 10. Potential Energy = -2.0135496e+07 Maximum force = 2.0486184e+12 on atom 4479 Norm of force = 7.2424045e+13 Again, symptomatic of severe atomic overlap. but again the same issue with table extent and still the production of pdb files. Any explanations? Investigate the starting configurations near the problematic atoms. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
Re: [gmx-users] Energy minimization Error
Ok now I have tryied to restart it all and the problem seems to be that the system has some overlapping. In fact, no matter what I freeze, water, CA or nothing, I get this error message VERSION 3.3.1 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. If you want to redistribute modifications, please consider that scientific software is very special. Version control is crucial- bugs must be traceable. We will be happy to consider code for inclusion in the official distribution, but derived work must not be called official GROMACS. Details are found in the README COPYING files. :-) gaia30 (-: Option Filename Type Description -sEM3.tpr InputGeneric run input: tpr tpb tpa xml -oEM3.trr Output Full precision trajectory: trr trj -xEM3.xtc Output, Opt! Compressed trajectory (portable xdr format) -cEM3.gro Output Generic structure: gro g96 pdb xml -eEM3.edr Output Generic energy: edr ene -gEM3.log Output Log file -dgdl EM3.xvg Output, Opt. xvgr/xmgr file -field EM3.xvg Output, Opt. xvgr/xmgr file -table EM3.xvg Input, Opt. xvgr/xmgr file -tablep EM3.xvg Input, Opt. xvgr/xmgr file -rerun EM3.trr Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpiEM3.xvg Output, Opt. xvgr/xmgr file -eiEM3.edi Input, Opt. ED sampling input -eoEM3.edo Output, Opt. ED sampling output -jEM3.gct Input, Opt. General coupling stuff -joEM3.gct Output, Opt. General coupling stuff -ffout EM3.xvg Output, Opt. xvgr/xmgr file -devout EM3.xvg Output, Opt. xvgr/xmgr file -runav EM3.xvg Output, Opt. xvgr/xmgr file -piEM3.ppa Input, Opt. Pull parameters -poEM3.ppa Output, Opt. Pull parameters -pdEM3.pdo Output, Opt. Pull data output -pnEM3.ndx Input, Opt. Index file -mtxEM3.mtx Output, Opt. Hessian matrix -dnEM3.ndx Output, Opt. Index file -coarse ION.gro InputGeneric trajectory: xtc trr trj gro g96 pdb Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 19 Set the nicelevel -deffnm stringEM3 Set the default filename for all file options -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -npint 1 Number of nodes, must be the same as used for grompp -ntint 1 Number of threads to start on each node -[no]v boolyes Be loud and noisy -[no]compact boolyes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np 1) -replexint 0 Attempt replica exchange every # steps -reseedint -1 Seed for replica exchange, -1 is generate a seed -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Back Off! I just backed up EM3.log to ./#EM3.log.2# Getting Loaded... Reading file EM3.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up EM3.edr to ./#EM3.edr.2# Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 200 ---inf, atom= 15321 Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 42875 ] Please report this to the mailing list (gmx-users@gromacs.org) --- With a Lead Filled Snowshoe (F. Zappa)
Re: [gmx-users] Energy minimization Error
On 11/02/2012 2:48 AM, francesca vitalini wrote: In fact in the reverse transformation I'm feeding the CG structure information. Yes, but you need a source of atomistic intra-residue knowledge about protein structure in order to convert a CG structure to something that is vaguely plausible at FG. Once I look through VMD to the FG structure I notice that the backbones are not in planes so definitely I need to run some minimization there. In the tutorial they were using simulating annealing, but I don't think I need more than energy minimization for that. What do you think? So you've learned that any kind of simple restraint based on the input FG structure is likely to produce a garbage result because the atomistic detail of the input FG structure is garbage. Simulated annealing does sound like a good way to start refining the structure. You need something capable of more than local minimization, unlike EM. Tiny time steps are probably necessary to cope with the large forces. In GROMACS 4.5 you could use some COM virtual sites (or similar, see manual) to have position restraints to the positions of the original beads. If you feel the result of the above refinement has deviated too much for whatever your real purpose is, then taking the refined structure and introducing such v-site position restraints could be useful. Mark 2012/2/10 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 11/02/2012 12:41 AM, francesca vitalini wrote: In order to overcome the problem I tried to fix everything except the backbone (solvent, sidechain and CA, as I want the structure to be maintained). However, if I do then I have problems with the energy minimization as the force on the 15300 is infinite. Getting Loaded... Reading file EM1-1.tpr, VERSION 3.3.1 (single precision) Loaded with Money Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 2000 --- inf, atom= 15300 Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648 tel:2147483648. It should have been within [ 0 .. 27744 ] Please report this to the mailing list (gmx-users@gromacs.org mailto:gmx-users@gromacs.org) --- Oh My God ! It's the Funky Shit (Beastie Boys) Halting program mdrun You suggested to check if there is any overlapping. ... so you need to get out some visualization software and look at the transformed structure :) There might be as my structure is obtained through a reverse transformation from a CG representation. In the mapping the atoms are positioned randomly in the bead. Now I'm running some energy minimization to equilibrate those atoms. I had to solvate the system after the mapping (couldn't do it before due to problems with ions)but I haven't equilibrated it yet and I'm keeping it fixed which could also be a source of overlapping. Local minimization with EM cannot in general take a random positioning of the generated atoms and make it one that will be stable under MD. Some structure knowledge needs to be build into the reverse transformation. Mark Any ideas? Thanks. Francesca 2012/2/10 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu francesca vitalini wrote: I achieve Steepest Descents converged to machine precision in 205 steps, but did not reach the requested Fmax 10. Potential Energy = -1.49131940478719e+07 Maximum force = 1.09664530279637e+06 on atom 1520 (parto of the protein) Norm of force = 2.28369808518165e+06 The magnitude of the force suggests atomic overlap somewhere. Start by investigating the environment around atom 1520. and the system looked with vmd doesn't look as if it was exploding. However, I have warnings about the table extension and I don't know why but gromacs writes pdb files sometime. However I thought that there The step.pdb files are written when mdrun is about to crash. might have been an error in the way I defined the
Re: [gmx-users] Energy minimization Error
On 11/02/2012 4:15 AM, francesca vitalini wrote: Ok now I have tryied to restart it all and the problem seems to be that the system has some overlapping. In fact, no matter what I freeze, water, CA or nothing, I get this error message VERSION 3.3.1 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. If you want to redistribute modifications, please consider that scientific software is very special. Version control is crucial- bugs must be traceable. We will be happy to consider code for inclusion in the official distribution, but derived work must not be called official GROMACS. Details are found in the README COPYING files. :-) gaia30 (-: Option Filename Type Description -sEM3.tpr InputGeneric run input: tpr tpb tpa xml -oEM3.trr Output Full precision trajectory: trr trj -xEM3.xtc Output, Opt! Compressed trajectory (portable xdr format) -cEM3.gro Output Generic structure: gro g96 pdb xml -eEM3.edr Output Generic energy: edr ene -gEM3.log Output Log file -dgdl EM3.xvg Output, Opt. xvgr/xmgr file -field EM3.xvg Output, Opt. xvgr/xmgr file -table EM3.xvg Input, Opt. xvgr/xmgr file -tablep EM3.xvg Input, Opt. xvgr/xmgr file -rerun EM3.trr Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb -tpiEM3.xvg Output, Opt. xvgr/xmgr file -eiEM3.edi Input, Opt. ED sampling input -eoEM3.edo Output, Opt. ED sampling output -jEM3.gct Input, Opt. General coupling stuff -joEM3.gct Output, Opt. General coupling stuff -ffout EM3.xvg Output, Opt. xvgr/xmgr file -devout EM3.xvg Output, Opt. xvgr/xmgr file -runav EM3.xvg Output, Opt. xvgr/xmgr file -piEM3.ppa Input, Opt. Pull parameters -poEM3.ppa Output, Opt. Pull parameters -pdEM3.pdo Output, Opt. Pull data output -pnEM3.ndx Input, Opt. Index file -mtxEM3.mtx Output, Opt. Hessian matrix -dnEM3.ndx Output, Opt. Index file -coarse ION.gro InputGeneric trajectory: xtc trr trj gro g96 pdb Option Type Value Description -- -[no]h bool no Print help info and quit -niceint 19 Set the nicelevel -deffnm stringEM3 Set the default filename for all file options -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -npint 1 Number of nodes, must be the same as used for grompp -ntint 1 Number of threads to start on each node -[no]v boolyes Be loud and noisy -[no]compact boolyes Write a compact log file -[no]sepdvdl bool no Write separate V and dVdl terms for each interaction type and node to the log file(s) -[no]multi bool no Do multiple simulations in parallel (only with -np 1) -replexint 0 Attempt replica exchange every # steps -reseedint -1 Seed for replica exchange, -1 is generate a seed -[no]glas bool no Do glass simulation with special long range corrections -[no]ionize bool no Do a simulation including the effect of an X-Ray bombardment on your system Back Off! I just backed up EM3.log to ./#EM3.log.2# Getting Loaded... Reading file EM3.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up EM3.edr to ./#EM3.edr.2# Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 200 ---inf, atom= 15321 Program mdrun, VERSION 3.3.1 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 42875 ] Please report this to the mailing list (gmx-users@gromacs.org
[gmx-users] Energy minimization Error
Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ;Include restraints on water #ifdef POSRES_WAT #include posre_wat.itp #endif ; Include generic topology for ions #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ;SOL 390842 SOL 390820 NA+22 while this is the posre_wat.itp file I generated with genrestr ; position restraints for non-Protein of Protein in water [ position_restraints ] ; i funct fcxfcyfcz 152311 1000 1000 1000 152321 1000 1000 1000 152331 1000 1000 1000 152341 1000 1000 1000 152351 1000 1000 1000 152361 1000 1000 1000 152371 1000 1000 1000 152381 1000 1000 1000 152391 1000 1000 1000 152401 1000 1000 1000 152411 1000 1000 1000 152421 1000 1000 1000 152431 1000 1000 1000 152441 1000 1000 1000 152451 1000 1000 1000 152461 1000 1000 1000 152471 1000 1000 1000 152481 1000 1000 1000 152491 1000 1000 1000 152501 1000 1000 1000 152511 1000 1000 1000 .. 1877121 1000 1000 1000
Re: [gmx-users] Energy minimization Error
francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. 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 Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ;Include restraints on water #ifdef POSRES_WAT #include posre_wat.itp #endif ; Include generic topology for ions #include /home/cocktail/vitalini/gromacs_special/share/gromacs/top/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ;SOL 390842 SOL 390820 NA+22 while this is the posre_wat.itp file I generated with genrestr ; position restraints for non-Protein of Protein in water [ position_restraints ] ; i funct fcxfcyfcz 152311 1000 1000 1000 152321 1000 1000 1000 152331 1000 1000 1000 152341 1000 1000 1000 152351 1000 1000 1000 152361 1000 1000 1000 152371 1000 1000 1000 152381 1000 1000 1000 152391 1000 1000 1000 152401 1000 1000 1000 152411 1000 1000 1000 152421 1000 1000 1000 152431
Re: [gmx-users] Energy minimization Error
Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? 2012/2/9 Justin A. Lemkul jalem...@vt.edu francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. 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_precisionhttp://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 Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/**gromacs_special/share/gromacs/** top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology #include /home/cocktail/vitalini/**gromacs_special/share/gromacs/** top/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ;Include restraints on water #ifdef POSRES_WAT #include posre_wat.itp #endif ; Include generic topology for ions #include /home/cocktail/vitalini/**gromacs_special/share/gromacs/** top/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 ;SOL 390842 SOL 390820 NA+22 while this is the posre_wat.itp file I generated with genrestr ; position restraints for non-Protein of Protein in water [ position_restraints ] ; i funct fcxfcyfcz 152311 1000 1000 1000 152321 1000 1000
Re: [gmx-users] Energy minimization Error
francesca vitalini wrote: Tryed the double precision without any success... Again the same type of error message. Might need to try other minimization algorithm. Any suggestions on that? What is the Fmax you achieve, and what are your intents for this process? Minimizing very low is only strictly necessary for certain types of very sensitive calculations. For normal MD, convergence below 100-1000 kJ/mol-nm is typical. Other algorithms are listed in the manual. They may or may not be necessary. -Justin 2012/2/9 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu francesca vitalini wrote: Hi all! I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation. So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file The other possibility is that there is no problem at all. Some systems cannot be minimized below certain thresholds, based on the input geometry. You may also want to try a different minimizer or double precision. 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 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 Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes define = -DEPOSRES ;define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 10.0 ; Stop minimization when the maximum force 1.0 kJ/mol dt = 0.005 ;nsteps = 2000 nsteps = 5000 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = System; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions epsilon_rf = 78 rcoulomb= 1.4 ; long range electrostatic cut-off rvdw= 1.4 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) table-extension = 1.2 and this is my topology ; ; File 'dynamin_dimer_fg.top' was generated ; By user: vitalini (213883) ; On host: goat ; At date: Mon Jan 30 11:02:21 2012 ; ; This is your topology file ; The Poodle Chews It (F. Zappa) ; ; Include forcefield parameters #include /home/cocktail/vitalini/__gromacs_special/share/gromacs/__top/ffG53a6m.itp ; Include chain topologies #include dynamin_dimer_fg_A.itp #include dynamin_dimer_fg_B.itp ; Include water topology
[gmx-users] Energy Minimization
Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in water (and with ions) separately and the copy coordinates and then process with NVT and NPT or run EM with restrained nanotubes of my system directly? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization
On 10/01/2012 9:54 PM, Steven Neumann wrote: Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in water (and with ions) separately and the copy coordinates and then process with NVT and NPT or run EM with restrained nanotubes of my system directly? The former is less likely to have problems. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization
Thank you. Should I also copy and paste coordinates of my ions or just my protein? Steven On Tue, Jan 10, 2012 at 11:03 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 9:54 PM, Steven Neumann wrote: Dear Gmx Users, I am setting up my simulations of carbon tube with protein. I solvated my system, added ions and I would like to run EM of my system. My carbons of the tube in MD will be restrained. In this case should I run EM of my protein in water (and with ions) separately and the copy coordinates and then process with NVT and NPT or run EM with restrained nanotubes of my system directly? The former is less likely to have problems. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization
On 10/01/2012 10:13 PM, Steven Neumann wrote: Thank you. Should I also copy and paste coordinates of my ions or just my protein? The randomly-placed ions will be immaterial for EM. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization
Thank you. Imagine I would like to put ligands in further simulations. Should I then copy coordinates of my ligands in smaller box (not to overlap my tube) and then copy both coordinates of ions and ligands plus protein? On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/01/2012 10:13 PM, Steven Neumann wrote: Thank you. Should I also copy and paste coordinates of my ions or just my protein? The randomly-placed ions will be immaterial for EM. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy Minimization
On 10/01/2012 10:46 PM, Steven Neumann wrote: Thank you. Imagine I would like to put ligands in further simulations. Should I then copy coordinates of my ligands in smaller box (not to overlap my tube) and then copy both coordinates of ions and ligands plus protein? Any way you want to construct your non-overlapping non-solvent non-ion molecules is fine. Previous EM of each is wise, but not necessarily required - vacuo EM is probably fine. Then solvate, then use genion, then EM the whole system. Copying ions from earlier calculations is a good way to generate atomic clashes, which is a high price to pay for randomly-placed ions that are different from those generated as above. Mark On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 10/01/2012 10:13 PM, Steven Neumann wrote: Thank you. Should I also copy and paste coordinates of my ions or just my protein? The randomly-placed ions will be immaterial for EM. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization error
Dear gromacs users, While doing energy minimization for a protein (from pdb), with oplsaa force field and tip4p water model, there was an error and em stopped - Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated What is the correction for this? Thanking you With regards kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization error
Kavyashree M wrote: Dear gromacs users, While doing energy minimization for a protein (from pdb), with oplsaa force field and tip4p water model, there was an error and em stopped - Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated What is the correction for this? Build a more reasonable starting structure. Somewhere you have atomic overlap or otherwise unresolvable geometry such that you have atoms flying across the system, as the error message indicates (although somewhat obliquely). The screen/log output from mdrun should print where the high forces are, or which atoms are having constraint problems, etc. Investigate these atoms in your starting structure and/or EM trajectory and determine an appropriate solution based on what you find. -Justin Thanking you With regards kavya -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization error
Ok thanks On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear gromacs users, While doing energy minimization for a protein (from pdb), with oplsaa force field and tip4p water model, there was an error and em stopped - Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated What is the correction for this? Build a more reasonable starting structure. Somewhere you have atomic overlap or otherwise unresolvable geometry such that you have atoms flying across the system, as the error message indicates (although somewhat obliquely). The screen/log output from mdrun should print where the high forces are, or which atoms are having constraint problems, etc. Investigate these atoms in your starting structure and/or EM trajectory and determine an appropriate solution based on what you find. -Justin Thanking you With regards kavya -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 30/01/11 16:13, David van der Spoel wrote: On 2011-01-30 17.08, ms wrote: Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. Oh, this is very bad news. Could you elaborate on that? (I have a CG model where this would be badly needed). With homogeneous I mean a solution of ions. Hmm, I would be happy to have more informations -that is, *why* should one try to avoid this? What artefacts/problems should I expect? Here: http://bit.ly/ig11UQ it seems that people use PME -with CHARMM here- to model efficiently non-neutral systems: As a result of including only the ion of interest in our simulations, the system will have a non-neutral charge. With particle-mesh Ewald electrostatics, this will result in a uniform neutralizing plasma [29] and [30]. In other words, a homogeneous neutralizing background charge is implicitly applied to the entire simulation space to avoid the divergence of the Ewald sum and to neutralize the system [29] and [30]. Although the background charge will alter the free energy profile, its effect can be shown to be negligible for a non-neutral charge of 2 e. The offset of the electrostatic free energy can be determined from [30] M.A. Kastenholz and P.H. Hünenberger, J. Phys. Chem. B 108 (2004), p. 774. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus (58)[30] Of course they may be horribly wrong, but they list some literature in support (which I'm going to check, but meanwhile...) Can spreading neutralizing charges along the other chain atoms be a viable alternative for enough atoms and enough low charge? (e.g. if I have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?) Sounds like a recipe for disaster. Uhm, given that mine is already a coarse-grained systems where practically all particles have 0 charge it could indeed change things badly. I've read this idea on one of the links of the mailing lists linked above in the thread. Try looking for solutions with explicit counter ions. That's exactly the point: I desperately need to *avoid* explicit counter ions. I don't want interactions between my systems and fake counterions. Thanks a lot, Massimo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 30/01/11 16:13, David van der Spoel wrote: On 2011-01-30 17.08, ms wrote: On 30/01/11 15:41, David van der Spoel wrote: Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. Oh, this is very bad news. Could you elaborate on that? (I have a CG model where this would be badly needed). Further info I found with a lazy check on gscholar: http://bit.ly/hzzvEx Although the stability of a trajectory is a necessary condition for studying equilibrium observables of a molecular system, it is not a sufficient one to guarantee their correctness. The use of lattice summation methods implies that periodicity in a system simulated under periodic boundary conditions is considered to be an intrinsic property of this system. We refer to this choice as Ewald boundary conditions (EWBC). There are a number of reasons to expect that the use of EWBC for simulating solutions may lead to undesirable side effects. [...] Finally, when a non-neutral solute is considered, the use of EWBC implicitly introduces a homogeneous background charge that neutralizes the unit cell. This charge density will not model realistically the charge density arising from a counter-ion atmosphere, because (i) it overlaps with solute atoms; (ii) it is independent of the distance to the surface of the solute molecule; and (iii) it completely neutralizes the solute charge within an arbitrary volume of solution, the volume of the unit cell. I would love to know how the way GROMACS does PME compares with this... thanks! m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 29/01/11 05:08, Matt Chan wrote: Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 2011-01-30 16.02, ms wrote: On 29/01/11 05:08, Matt Chan wrote: Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. Gromacs does not ignore any terms in the simulations if I am not mistaken. It also computes PME at every step in contrast to NAMD (don't know about Amber). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 30/01/11 15:41, David van der Spoel wrote: My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. Oh, this is very bad news. Could you elaborate on that? (I have a CG model where this would be badly needed). Can spreading neutralizing charges along the other chain atoms be a viable alternative for enough atoms and enough low charge? (e.g. if I have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?) From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. Gromacs does not ignore any terms in the simulations if I am not mistaken. It also computes PME at every step in contrast to NAMD (don't know about Amber). Thanks. m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 2011-01-30 17.08, ms wrote: On 30/01/11 15:41, David van der Spoel wrote: My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. Oh, this is very bad news. Could you elaborate on that? (I have a CG model where this would be badly needed). With homogeneous I mean a solution of ions. Can spreading neutralizing charges along the other chain atoms be a viable alternative for enough atoms and enough low charge? (e.g. if I have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?) Sounds like a recipe for disaster. Try looking for solutions with explicit counter ions. From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. Gromacs does not ignore any terms in the simulations if I am not mistaken. It also computes PME at every step in contrast to NAMD (don't know about Amber). Thanks. m. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] energy minimization of a charged system in vacuum
Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Thanks in advance for your replies, -- Matthew Chan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization of a charged system in vacuum
Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization
Hi all, I am minimizing my protein (230 amino acids) with the minim.mdp file given in the lysozyme tutorial but I am not getting a stable graph .. I checked the manual also to look for parameters but I am not able to find such information there apart from the theory about the minimzation algos and process.. So can anybody direct me to some relevant link or help me out in this regard ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
Can you provide more details ? Which graph are you talking about ? Amit On Mon, Jan 17, 2011 at 12:05 AM, bharat gupta bharat.85.m...@gmail.comwrote: Hi all, I am minimizing my protein (230 amino acids) with the minim.mdp file given in the lysozyme tutorial but I am not getting a stable graph .. I checked the manual also to look for parameters but I am not able to find such information there apart from the theory about the minimzation algos and process.. So can anybody direct me to some relevant link or help me out in this regard ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
I am doin the first minimization step.. here are the details of 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) -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
OK what seemed wrong to you? On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta bharat.85.m...@gmail.comwrote: I am doin the first minimization step.. here are the details of 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) -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
The potential energy graph is not coming parallel to x-axis is getting down towars the x-axis .. normally it should be paralle to x-axis.. -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
Check your log file to see if the minimization criterion was satisfied ie the max force is less than emtol. On Mon, Jan 17, 2011 at 12:29 AM, bharat gupta bharat.85.m...@gmail.comwrote: The potential energy graph is not coming parallel to x-axis is getting down towars the x-axis .. normally it should be paralle to x-axis.. -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization
bharat gupta wrote: The potential energy graph is not coming parallel to x-axis is getting down towars the x-axis .. normally it should be paralle to x-axis.. Depending on how quickly the potential energy converges, it may or may not. The most important outcome of EM is that you achieve reasonable values of the potential and the maximum force. -Justin -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] eNERGY mINIMIZATION
Hi, I did the energy minimization of my protein (230 amino acids) after adding ions .. and after checking the potential energy of the system I was getting thee graph which is different from the one given in the lysozyme tutorial i.e. the the potential line in graph is not parallel to the x axix.. Here is are conditions that I used for minimization : define = -DFLEX_SPC constraints = none integrator = steep nsteps = 5 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no I got the following result :- Steepest Descents converged to Fmax 2000 in 296 steps Potential Energy = -6.9540075e+05 Maximum force = 1.9863752e+03 on atom 1669 Norm of force = 3.7864201e+01 -- I want to know which parameters are important to get a correct minimized structure and what value do I have to take for emtol and nsteps to minimize the structure properly.. Also how would I know that at what value of emtol my protein will be minimized.. I checked the manual to get some details but there only the basic theory of minimzation is written.. A detailed explanation will be more helpful... -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] eNERGY mINIMIZATION
On 18/01/2011 2:50 PM, bharat gupta wrote: Hi, I did the energy minimization of my protein (230 amino acids) after adding ions .. and after checking the potential energy of the system I was getting thee graph which is different from the one given in the lysozyme tutorial i.e. the the potential line in graph is not parallel to the x axix.. You're comparing apples and oranges... maybe lysozyme is already pretty close to the minimum. Consider the axis scales, also. Note that the energy change per EM step doesn't have any physical meaning. Here is are conditions that I used for minimization : define = -DFLEX_SPC constraints = none integrator = steep nsteps = 5 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no I got the following result :- Steepest Descents converged to Fmax 2000 in 296 steps Potential Energy = -6.9540075e+05 Maximum force = 1.9863752e+03 on atom 1669 Norm of force = 3.7864201e+01 -- I want to know which parameters are important to get a correct minimized structure and what value do I have to take for emtol and nsteps to minimize the structure properly.. Also how would I know that at what value of emtol my protein will be minimized.. How long should a piece of string be? Your PE is OK, so if you reduce emtol then you can reduce the maximum force. This will prolong the EM if you think you need to do that. I checked the manual to get some details but there only the basic theory of minimzation is written.. A detailed explanation will be more helpful... The purpose of EM is normally to relieve bad contacts, fill solvent voids, etc. Do something plausible (like you've done) and then try the next step. If you get problems there, go back and do EM harder (among other strategies) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] eNERGY mINIMIZATION
Sir, That's what I want to know how u found out that the P.E. is ok and then what about the PE graph ?? Does it has to be some what parallel to x-axis in case of every minimized structure as in my case its not parallel to x-axis , rather its getting down towards the x-axis.. ... generally for a miminized structure how it should be ?? ... I again carried out the minimzation with emtol = 1000 and the values of PE and max force are Steepest Descents converged to Fmax 1000 in 826 steps Potential Energy = -7.1715738e+05 Maximum force = 9.6300812e+02 on atom 1669 Norm of force = 2.0939770e+01 -- Correct me if I am wrong ... If the Fmax Emtol , it means that the structure is minimized ?? One more thing I want to know .. since we are changing the topol file also while minimzation then the repitition of minimization again would lead to any drastic changes to the topology or not .. as in my case I first did with emtol = 2000 and then with emtol = 1000 ?? --- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] eNERGY mINIMIZATION
On 18/01/2011 3:12 PM, bharat gupta wrote: Sir, That's what I want to know how u found out that the P.E. is ok and then what about the PE graph ?? A value of large magnitude and negative sign is probably OK. Exactly how large varies widely with system composition, force field, etc. So nobody worries much about this. Does it has to be some what parallel to x-axis in case of every minimized structure as in my case its not parallel to x-axis , rather its getting down towards the x-axis.. ... generally for a miminized structure how it should be ?? Like I said last time, the apparent gradient is not physical, so don't stress about it. The physical things are the magnitude of the energy, and the magnitude of the force. ... I again carried out the minimzation with emtol = 1000 and the values of PE and max force are Steepest Descents converged to Fmax 1000 in 826 steps Potential Energy = -7.1715738e+05 OK, so this is a bit lower. Maybe you could go further. Maybe it's enough already. That depends on your purpose, but for simulation preparation, see my previous email. Maximum force = 9.6300812e+02 on atom 1669 Norm of force = 2.0939770e+01 -- Correct me if I am wrong ... If the Fmax Emtol , it means that the structure is minimized ?? Check out manual section 7.3.5. One more thing I want to know .. since we are changing the topol file also while minimzation then the repitition of minimization again would lead to any drastic changes to the topology or not .. as in my case I first did with emtol = 2000 and then with emtol = 1000 ?? EM is fast, so you may as well just start from your original structure each time, so you have a simple workflow. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization - single/double precision
Dear Gromacs users, I wanted to know whether it is correct doing minimization in double precision and rest all - pdb2gmx, editconf, genbox, grompp and mdrun itself in single precision. I had got convergence during energy minimization using double precision but not single precision (input files for both were same and prepared using single precision). Thanks in advance MKS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization query
Hi, I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly same parameters which i use for monomer during dimer minimisation in solvent. System Details: # Atoms = 4488 (# Res = 582) octahedron box with d = 0.9 Solvent (spce water model) density = 1050.6 g/L (During monomer MD it was 1048.86 g/L) System subjected to energy minimisation, Only warning arising during grompp: --- WARNING 1 [file dimer.top, line 46]: 86974 non-matching atom names atom names from dimer.top will be used atom names from neutral.pdb will be ignored --- This was neglected using -maxwarn option and contd... Error during minimisation run (mdrun): --- Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Step= 14, Dmax= 1.2e-06 nm, Epot= 7.04150e+23 Fmax= inf, atom= 37 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 6.9065950e+23 Maximum force =inf on atom 37 Norm of force =inf - 1) I thought that the box size is too small so that dimer is not able to move at all and hence the energy is too high. But I am getting same error even if box size is increased to 2.0 nm 2) I checked my initial structure and even the neutralised structure post solvation only to find that it is not broken. (My system has a missing loop which I have modeled using modeler9v8 and then subjected it to MD in solvent.) What could possibly go wrong ? Could it be really the step size or precision although I do not think so ! Regards, Nikhil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization query
Nikhil, I had a similar problem, and was getting the same error. In my case the order of my atoms was different in my pdb/gro and my top/itp file. This made my system do a weird inversion, due to incorrect placement of atoms. And my energies were terrible. Hope this helps, TJ Mustard On December 28, 2010 at 8:26 AM nikhil damle pdnik...@yahoo.co.in wrote: Hi, I am trying to simulate a dimeric structure and I have already simulated its monomeric form. I use exactly same parameters which i use for monomer during dimer minimisation in solvent. System Details: # Atoms = 4488 (# Res = 582) octahedron box with d = 0.9 Solvent (spce water model) density = 1050.6 g/L (During monomer MD it was 1048.86 g/L) System subjected to energy minimisation, Only warning arising during grompp: --- WARNING 1 [file dimer.top, line 46]: 86974 non-matching atom names atom names from dimer.top will be used atom names from neutral.pdb will be ignored --- This was neglected using -maxwarn option and contd... Error during minimisation run (mdrun): --- Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 14, Dmax= 1.2e-06 nm, Epot= 7.04150e+23 Fmax= inf, atom= 37 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 6.9065950e+23 Maximum force = inf on atom 37 Norm of force = inf - 1) I thought that the box size is too small so that dimer is not able to move at all and hence the energy is too high. But I am getting same error even if box size is increased to 2.0 nm 2) I checked my initial structure and even the neutralised structure post solvation only to find that it is not broken. (My system has a missing loop which I have modeled using modeler9v8 and then subjected it to MD in solvent.) What could possibly go wrong ? Could it be really the step size or precision although I do not think so ! Regards, Nikhil TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy Minimization
Hi all, I am using CHARMM forcefield with tables for Protein SOL interactions for alanine dipeptide. Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard tables for 6-12 interactions used) Combination rule changed from '2' to '1' in forcefield.itp file. In the energy minimization step, using mdrun the following problem is encountered: Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e+00 Number of steps=1 F-max = 2.98523e+10 on atom 4 F-Norm= 1.32072e+09 step -1: Water molecule starting at atom 1149 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates title = Energy Minimization ; Title of run ; The following line tell the program the standard locations where to find certain files cpp = /lib/cpp ; Preprocessor ; Define can be used to control processes ;define = -DFLEXIBLE define = -DPOSRES ; Parameters describing what to do, when to stop and what to save integrator = cg; Algorithm (steep = steepest descent minimization) emtol = 1.0 ; Stop minimization when the maximum force 1.0 kJ/mol nsteps = 1 ; Maximum number of (minimization) steps to perform nstenergy = 1 ; Write energies to disk every nstenergy steps energygrps = Protein SOL energygrp_table = Protein SOL ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = User ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off constraints = none ; Bond types to replace by constraints pbc = xyz ; Periodic Boundary Conditions (yes/no) Any suggestions? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization by keeping heavy atom fixed
I have a protein structure determined by x-ray crystallography method where hydrogen atoms were missing. I have added hydrogen atom. Now i need to do energy minimization of this protein by keeping the heavy atom fixed at their crystallographic position. How can I manage which atoms to be fixed and which to keep flexible during EM and MD. Thanks all -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy minimization by keeping heavy atom fixed
- Original Message - From: priyabrata panigrahi priyabra...@gmail.com Date: Thursday, August 26, 2010 17:09 Subject: [gmx-users] Energy minimization by keeping heavy atom fixed To: gmx-users@gromacs.org I have a protein structure determined by x-ray crystallography method where hydrogen atoms were missing. I have added hydrogen atom. Now i need to do energy minimization of this protein by keeping the heavy atom fixed at their crystallographic position. How can I manage which atoms to be fixed and which to keep flexible during EM and MD. The mechanism is called position restraints and you should read about that in the manual. pdb2gmx will help generate the necessary file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy minimization: problems with ramachanrad score
This does not imply that less EM is better than more EM. It implies that the native structure is not necessarily in an absolute energy minimum according to our FF's. This is certainly true. We could take the point of view that when an experimentalist refers to as a native structure is actually a model that fits a particular electron density map and another crystal form is bound to differ, but I guess we all know that our FF's are less accurate than this difference so it's probably a moot point. EM with MM FF's is not rubbish. It's important and it has its place. So randomizing a structure and running EM doesn't take you back to the original minimum? sure, this is why we call the energy surface rugged. To get back to your homology modeling, I would always suspect that you will need to run MD in order to explore conformational space. Homology modeling is not my strong suit, but I've seen cases experimentally where a single amino acid mutation can destabilize a folded protein and cause it to be unfolded (and vice-versa), so in that light I'm still astounded that homology modeling works at all. Sorry to be a little vague, but then again you didn't really ask a specific question, unless plasmatic is a real word... Chris. -- original message -- I 'm trying to relax my homology models from steric clashes, and while searching for the appropriate minimization scheme, I came across this old thread: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027043.html The authors in the cited paper have created near-native structures as a test set with RMSD 1.06 ± 0.14 Å over the native ones. Then they ran energy minimization in vacuo with l-bfgs for 1 steps or until convergence to machine precision and they found that ordinary MM potentials (AMBER99, OPLS-AA, GROMOS96, and ENCAD) showed no significant improvement on the structures. On the contrary the last 3 were found to move the conformation away from the native state by 11%, 40%, and 44% respectively. They also tested their own 3 hybrid Knowledge-Based / Molecular Mechanics (KB/MM) potentials and found that the best performing was moving the structures by 11% closer to the native fold. Essentially they claimed that energy minimization with the ordinary MM potentials is rubbish! I have one remark to make on this. Their decoy set comprised no-native protein conformers with RMSD ~1A. I'm wondering if the results will be similar for RMSDs ~3A as in my case where I'm building homology models with average sequence identity to templates 25-30%? And with respect to the original question, if you overdo it with energy minimization the Ramachandran scores do deteriorate. However if you stop at an intermediate step you can get the same score, bond lengths and angles but with less steric clashes. Is this improvement plasmatic as the authors claim, namely you have moved away from the native fold although stereochemically the model look good? -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100617/aafe7f09/attachment.html Previous message: [gmx-users] Electric field, potential, dielectric constant Next message: [gmx-users] Energy minimization: problems with ramachanrad score Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the gmx-users mailing list -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy minimization: problems with ramachanrad score
I 'm trying to relax my homology models from steric clashes, and while searching for the appropriate minimization scheme, I came across this old thread: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027043.html The authors in the cited paper have created near-native structures as a test set with RMSD 1.06 ± 0.14 Å over the native ones. Then they ran energy minimization in vacuo with l-bfgs for 1 steps or until convergence to machine precision and they found that ordinary MM potentials (AMBER99, OPLS-AA, GROMOS96, and ENCAD) showed no significant improvement on the structures. On the contrary the last 3 were found to move the conformation away from the native state by 11%, 40%, and 44% respectively. They also tested their own 3 hybrid Knowledge-Based / Molecular Mechanics (KB/MM) potentials and found that the best performing was moving the structures by 11% closer to the native fold. Essentially they claimed that energy minimization with the ordinary MM potentials is rubbish! I have one remark to make on this. Their decoy set comprised no-native protein conformers with RMSD ~1A. I'm wondering if the results will be similar for RMSDs ~3A as in my case where I'm building homology models with average sequence identity to templates 25-30%? And with respect to the original question, if you overdo it with energy minimization the Ramachandran scores do deteriorate. However if you stop at an intermediate step you can get the same score, bond lengths and angles but with less steric clashes. Is this improvement plasmatic as the authors claim, namely you have moved away from the native fold although stereochemically the model look good? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy minimization: problems with ramachanrad score
- Original Message - From: Thomas Evangelidis teva...@gmail.com Date: Thursday, June 17, 2010 10:48 Subject: [gmx-users] Energy minimization: problems with ramachanrad score To: gmx-users@gromacs.org I 'm trying to relax my homology models from steric clashes, and while searching for the appropriate minimization scheme, I came across this old thread: http://lists.gromacs.org/pipermail/gmx-users/2007-April/027043.html The authors in the cited paper have created near-native structures as a test set with RMSD 1.06 ± 0.14 Å over the native ones. Then they ran energy minimization in vacuo with l-bfgs for 1 steps or until convergence to machine precision and they found that ordinary MM potentials (AMBER99, OPLS-AA, GROMOS96, and ENCAD) showed no significant improvement on the structures. On the contrary the last 3 were found to move the conformation away from the native state by 11%, 40%, and 44% respectively. They also tested their own 3 hybrid Knowledge-Based / Molecular Mechanics (KB/MM) potentials and found that the best performing was moving the structures by 11% closer to the native fold. Essentially they claimed that energy minimization with the ordinary MM potentials is rubbish! I have one remark to make on this. Their decoy set comprised no-native protein conformers with RMSD ~1A. I'm wondering if the results will be similar for RMSDs ~3A as in my case where I'm building homology models with average sequence identity to templates 25-30%? And with respect to the original question, if you overdo it with energy minimization the Ramachandran scores do deteriorate. However if you stop at an intermediate step you can get the same score, bond lengths and angles but with less steric clashes. Is this improvement plasmatic as the authors claim, namely you have moved away from the native fold although stereochemically the model look good? Without having actually read their paper... there's could easily be a kind of apples-and-oranges comparison going on. The local optimum resulting from a single EM using MM forcefields optimized for non-vacuum conditions on near-native folds in vacuo are being compared with (say) crystal structures for the fitness of those minima as a model of (presumably) what's around under biological conditions. I'd guess that there's an appreciable number of cases where this is a three-way absurdity... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy minimization: problems with ramachanrad score
Without having actually read their paper... there's could easily be a kind of apples-and-oranges comparison going on. The local optimum resulting from a single EM using MM forcefields optimized for non-vacuum conditions on near-native folds in vacuo are being compared with (say) crystal structures for the fitness of those minima as a model of (presumably) what's around under biological conditions. I'd guess that there's an appreciable number of cases where this is a three-way absurdity... With respect to the MM forcefields optimized for aqua conditions, isn't it more reasonable to minimize the homology models in a waterbox? After all that the native conformation is in aqua solution. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy minimization: problems with ramachanrad score
The implicit water models were built in a time when computing time was limiting because of the computing power if this epoch. But now is feasible to do simulations with explicit water. Maybe one should argue that at the first minimization of a protein waterbox the waters are not in the natural position, but there is not a natural position for a water, there is an ensemble of positions that we can explore with a MD. Minimization is to remove severe clashes between atoms, but the prediction of an homology model should end with an MD, and then one can get an average structure and minimize it, to get the homology model. Best regards. Lucio Montero PhD. student Insituto de Biotecnologia, UNAM, Mexico Mensaje citado por Thomas Evangelidis teva...@gmail.com: Without having actually read their paper... there's could easily be a kind of apples-and-oranges comparison going on. The local optimum resulting from a single EM using MM forcefields optimized for non-vacuum conditions on near-native folds in vacuo are being compared with (say) crystal structures for the fitness of those minima as a model of (presumably) what's around under biological conditions. I'd guess that there's an appreciable number of cases where this is a three-way absurdity... With respect to the MM forcefields optimized for aqua conditions, isn't it more reasonable to minimize the homology models in a waterbox? After all that the native conformation is in aqua solution. -- Lucio Ricardo Montero Valenzuela Estudiante de doctorado en Ciencias Bioquímicas Lab. del Dr. Federico Sánchez Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization + freeze atoms
Hello, I am trying to do energy minimization with normal mode analysis for my ststem. I used freezegrps and freezedim optitions to freeze the atoms. I found that after minimization the atoms are moved. Can you tell me how to freeze atoms for energy minimzation. I need this geometry for normal mode analysis. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization + freeze atoms
Hello, I am trying to do energy minimization with normal mode analysis for my ststem. I used freezegrps and freezedim optitions to freeze the atoms. I found that after minimization the atoms are moved. Can you tell me how to freeze atoms for energy minimzation. I need this geometry for normal mode analysis. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization - infinite force on atom
Hi gmx-users I am somehow famliar with gromacs but only used it with coarse grained force fields (Martini) so far, not with all atom ones. I am now trying to run a simulation on a membrane protein system (protein embedded in a POPC bilayer solvated with water) using the gromos force field (Gromacs 4.0.2 ffG53a). Using gromacs tutorials I managed to create the required input files (.gro, .top and .itp). I at at the stage of running a energy minimization using position restraints on the protein and the peptide molecules. I can grompp the input files grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx with the following input file: -- - define = -DPOSRES -DPOSRES_LIPID integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; 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 = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) --- and the following topology file --- ; Include forcefield parameters #include ffG53a6_lipid.itp ; Include chain topologies #include protein.itp ; Include Position restraint file #ifdef POSRES #include posre_protein.itp #endif ; Include POPC topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include spc.itp ; Include generic topology for ions #include ions.itp [ system ] ; Name mscl protein with POPC bilayer [ molecules ] ; Compound#mols Protein 1 POPC242 SOL 32145 CL- 91 NA+ 91 --- When I run the simulation I get the following output after 16 steps of the minimisation --- Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 16 steps, but did not reach the requested Fmax 100. Potential Energy = 8.0175742e+17 Maximum force =inf on atom 4443 Norm of force =inf --- It seems there is an infinite force on atom 4443 but I don't really understand what that means. The confout.gro structure looks ok ie the system has not exploded. Should the protein not be restrained? How do I know my position restraints actually work? I tried increasing the force constant of the restraints or removing the restraints but still get the same output. I also tried adding -DFLEXIBLE since I am using the spc model, but still the same output. can anyone tell me what that message actually means and what is wrong with my system? thanks -- Evelyne Deplazes PhD student Theoretical Chemistry group University of Western Australia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization - infinite force on atom
On 8/04/2010 4:23 PM, Evelyne Deplazes wrote: Hi gmx-users I am somehow famliar with gromacs but only used it with coarse grained force fields (Martini) so far, not with all atom ones. I am now trying to run a simulation on a membrane protein system (protein embedded in a POPC bilayer solvated with water) using the gromos force field (Gromacs 4.0.2 ffG53a). Using gromacs tutorials I managed to create the required input files (.gro, .top and .itp). I at at the stage of running a energy minimization using position restraints on the protein and the peptide molecules. I can grompp the input files grompp -f min_posre.mdp -p topol.top -c system.gro -o topol.tpr -n index.ndx with the following input file: -- - define = -DPOSRES -DPOSRES_LIPID integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; 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 = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.2 ; Short-range electrostatic cut-off rvdw= 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) --- and the following topology file --- ; Include forcefield parameters #include ffG53a6_lipid.itp ; Include chain topologies #include protein.itp ; Include Position restraint file #ifdef POSRES #include posre_protein.itp #endif ; Include POPC topology #include popc.itp #ifdef POSRES_LIPID #include lipid_posre.itp #endif ; Include water topology #include spc.itp ; Include generic topology for ions #include ions.itp [ system ] ; Name mscl protein with POPC bilayer [ molecules ] ; Compound#mols Protein 1 POPC242 SOL 32145 CL- 91 NA+ 91 --- When I run the simulation I get the following output after 16 steps of the minimisation --- Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. Steepest Descents converged to machine precision in 16 steps, but did not reach the requested Fmax 100. Potential Energy = 8.0175742e+17 Maximum force =inf on atom 4443 Norm of force =inf --- It seems there is an infinite force on atom 4443 but I don't really understand what that means. The confout.gro structure looks ok ie the system has not exploded. Should the protein not be restrained? How do I know my position restraints actually work? I tried increasing the force constant of the restraints or removing the restraints but still get the same output. I also tried adding -DFLEXIBLE since I am using the spc model, but still the same output. can anyone tell me what that message actually means and what is wrong with my system? A useful diagnostic will be to remove the attempts to use position restraints in the define = line. If you still get an error like this, then your problem (massive positive energy, infinite forces) is almost certainly a severe atomic overlap, possibly near atom 4443. If so, get out a visualization program and look for water overlapping lipid, or something. Position restraints won't help resolve gross errors like that... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization in charged systems
Hi all, I am trying to simulate a electroosmotic flow in a nanochannel. System consists of water + (Cl-) ions in a channel confined of silicon 111 walls. I start with taking water as only solvent, equilibrating the system for about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-) ions. Walls are charged appropriately to maintain electro-neutrality in the system. The problem is with Energy minimization after inserting ions using steep algorithm (haven't turned on the electric field yet). I am getting an error like this: t = 0.038 ps: Water molecule starting at atom 2569 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates and Steepest Descents converged to machine precision in 88 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.75456106043895e+06 Maximum force = 1.07111309902475e+11 on atom 4898 Norm of force = 1.48772609239112e+09 If it were only couple of such molecules, I could have removed them easily from the gro file. The problem is twofold, there are around 10 molecules which give this error message, plus even after removal of these molecules, energy minimization results in the same error on different sets of molecules. I have tried a number of ways to tackle this including tuning the time step. Is there any way to avoid this? Any help would be appreciated. Thanks in advance. -- Ravi Bhadauria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] energy minimization in charged systems
What are the atoms that are causing the problems actually doing, where are they located etc? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ravi Bhadauria Sent: Thursday, 8 April 2010 3:11 PM To: gmx-users@gromacs.org Subject: [gmx-users] energy minimization in charged systems Hi all, I am trying to simulate a electroosmotic flow in a nanochannel. System consists of water + (Cl-) ions in a channel confined of silicon 111 walls. I start with taking water as only solvent, equilibrating the system for about 12-15 ps (gmxcheck runs clean), and then use genion to insert (Cl-) ions. Walls are charged appropriately to maintain electro-neutrality in the system. The problem is with Energy minimization after inserting ions using steep algorithm (haven't turned on the electric field yet). I am getting an error like this: t = 0.038 ps: Water molecule starting at atom 2569 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates and Steepest Descents converged to machine precision in 88 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.75456106043895e+06 Maximum force = 1.07111309902475e+11 on atom 4898 Norm of force = 1.48772609239112e+09 If it were only couple of such molecules, I could have removed them easily from the gro file. The problem is twofold, there are around 10 molecules which give this error message, plus even after removal of these molecules, energy minimization results in the same error on different sets of molecules. I have tried a number of ways to tackle this including tuning the time step. Is there any way to avoid this? Any help would be appreciated. Thanks in advance. -- Ravi Bhadauria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization of a box containing two Na+ ions and water does not converge
Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the script below, but it did not converge. After that, I removed one of the ions, and tried again, it did not work again. I am using ffG43a1 ff, and checked whether I used the correct naming for the ion: Everything seems to be OK. I could not attach the initial coordinate file due to the limited size. If you want I can also sent it to you as well. *Script: * title = Minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 3 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off coulombtype = PME rcoulomb= 1.0 rvdw= 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 *Output*: Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 100. Potential Energy = -1.0409969e+05 Maximum force = 9.6685031e+04 on atom 294 Norm of force = 1.4924829e+03 What may be the problem? Best Regards -- Ozge Engin ★☆ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization of a box containing two Na+ ions and water does not converge
Ozge Engin wrote: Hi all, I have been trying to calculate the PMF of two NA+ ions in explicit bulk water. First, I tried to calculate the mean force between the two ions at a distance of 0.48 nm, which is big enough than the diameter of the ions. I first energy minimized the system with the script below, but it did not converge. After that, I removed one of the ions, and tried again, it did not work again. I am using ffG43a1 ff, and checked whether I used the correct naming for the ion: Everything seems to be OK. Irrelevant. If naming were an issue, grompp would have failed with a fatal error. I could not attach the initial coordinate file due to the limited size. If you want I can also sent it to you as well. *Script: * title = Minimization cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 3 nstlist = 10 ns_type = grid rlist = 1.0 vdwtype = cut-off coulombtype = PME rcoulomb= 1.0 rvdw= 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 100.0 emstep = 0.01 *Output*: Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 100. Potential Energy = -1.0409969e+05 Maximum force = 9.6685031e+04 on atom 294 Norm of force = 1.4924829e+03 What may be the problem? Not a clue. What is atom 294? Look at the output - what are the other nearby atoms that could be causing the excessive force? -Justin Best Regards -- Ozge Engin ★☆ -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization
Hi gromacs users I want to study interaction of protein-dna by gromacs. For energy minimization, is using of only 1 algorithm, for example steepest descent or conjugate gradient, enough? How many steps is necessary for EM? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
