Re: [gmx-users] topology for small peptide using amber03
PDB format has fixed column widths. You cannot edit it correctly unless you preserve the layout - e.g. replace deleted characters with spaces. Mark On Nov 28, 2013 4:26 AM, "kolnkempff" wrote: > /I am trying to use pdb2gmx to get a topology for a very simple peptide > that > has just three components: an ACE residue followed by phenylananine > followed by NME > I've read through the Duan article and it seems that amber03 should be > ideal > for this. The pdb file I'm using came from a quantum simulation using > gamess. I went in by hand to label each atom as belonging to ACE, PHE, or > NME. > > Try #1 All atoms listed as "HETATM"/ > > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.r2b > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.r2b > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.r2b > Reading apn1.pdb... > WARNING: all CONECT records are ignored > Read 'UNNAMED', 32 atoms > Analyzing pdb file > Splitting chemical chains based on TER records or chain id changing. > There are 1 chains and 0 blocks of water and 1 residues with 32 atoms > > chain #res #atoms > 1 ' ' 3 32 > > All occupancies are one > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (amber03) > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.rtp > Residue 93 > Sorting it all out... > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.rtp > Residue 109 > Sorting it all out... > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.rtp > Residue 125 > Sorting it all out... > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.hdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.hdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.hdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.n.tdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.c.tdb > Processing chain 1 (32 atoms, 3 residues) > Identified residue PHE1 as a starting terminus. > Identified residue NME1 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/aminoacids.arn > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/dna.arn > Opening force field file > /usr/local/gromacs/share/gromacs/top/amber03.ff/rna.arn > > --- > Program pdb2gmx, VERSION 4.6.4 > Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/pdb2gmx.c, line: > 727 > > Fatal error: > Atom H in residue ACE 1 was not found in rtp entry ACE with 6 atoms > while sorting atoms. > > /I looked at aminoacids.rtp which lists [ACE] as having 6 atoms. I went > ahead and checked [PHE] and [NME] and I have the same number and type of > atoms as they do. > > Try #2. After looking at a pdb file for a small neuropeptide I decided to > try labeling everything as "ATOM" rather than 'HETATM" > [first part is same as before]/ > > Warning: Starting residue E1 in chain not identified as Protein/RNA/DNA. > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > > --- > Program pdb2gmx, VERSION 4.6.4 > Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/resall.c, line: > 642 > > Fatal error: > Residue 'E' not found in residue topology database > > /Try #3. I labeled the phenylalanine atoms as "ATOM" and the terminal ACE > and NME atoms as "HETATM"/ > Warning: Starting residue E1 in chain not identified as Protein/RNA/DNA. > Identified residue ACE1 as a starting terminus. > Identified residue NME1 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > > --- > Program pdb2gmx, VERSION 4.6.4 > Source code file: /home/koln/bin/gromacs-4.6.4/src/kernel/resall.c, line: > 642 > > Fatal error: > Residue 'E' not found in residue topology database > > /I have no idea where "Residue 'E'" came from. > Since the third try seems to be closest to "working", that's the one I am > including below. > > Thanks in advance for whatever help you can offer. > > Koln/ > > pdb file:COMPNDUNNAMED > AUTHORGENERATED BY OPEN BABEL 2.3.1 > ATOM1 N PHE 1 0.720 0.859 -0.499 1.00 0.00 > N > ATOM2 C PHE 1 0.760 -0.439 0.174 1.00 0.00 > C > ATOM3 C PHE 1 2.125 -1.161 0.111 1.00 0.00 > C > ATOM4 O PHE 1
Re: [gmx-users] step 0Segmentation fault: 11
Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a segmentation fault. GROMACS doesn't waste its time checking for this, since that would hurt everyone's performance and gain only a descriptive error that something is horribly broken! Mark On Nov 28, 2013 1:36 AM, "Valentina" wrote: > I still cannot resolve this problem. Is there any way to find out what is > causing Segmentation Fault? Normally Gromacs provides quite comprehendible > errors, but this one. > > I have checked the charges against DFT. > > I also have the output of the system simulated with Discover. I am using > that force field (obviously tabulated) and charges used there. > > The initial model is taken from Xray and optimised with DFT. > > Still md.log terminates with unrealistic T & P on 0th step: > > / Step Time Lambda > 00.00.0 > > > Grid: 4 x 3 x 3 cells >Energies (kJ/mol) > Tab. BondsTab. AnglesLJ (SR) Coulomb (SR) Potential > 5.44943e+064.41001e+119.86202e+02 -2.42548e+054.41006e+11 > Kinetic En. Total Energy Conserved En.Temperature Pressure (bar) > 1.97584e+161.97588e+161.97588e+162.24716e+151.99874e+16 > / > > > BTW - I noticed that I get continuously get a 0 dimension in z direction if > I do energy minimisation with plc = xy - is that right? > > My equil.mdp is following - may be some problem there? > I do energy minimisation before equilibration. > > /integrator = md > nsteps = 100 > dt = 0.001 > ;comm_mode = ANGULAR > nstenergy= 1 > nstxout = 1 > nstvout = 1 > energygrps = System > ; cut-offs at 1nm > rlist= 0.8 > nstlist = 10 > coulombtype = user > rcoulomb = 0.8 > vdw-type = user > rvdw = 0.8 > pbc = xyz > periodic_molecules = yes > ; set temperature to 300K > tcoupl = V-rescale > tc-grps = System > tau-t= 1.0 > ref-t= 500 > ; and pressure to 1 bar > pcoupl = no > compressibility = 4.5e-5 > ; generate initial velocities > gen-vel = no/ > > I am running with 6-9 LJ, that I provide input to mdrun > > > > > I do energy minimisation before equilibration. > em.mdp is > /integrator = steep > nsteps = 50 > emtol= 1 > emstep = 0.001 > nstxout = 1 > nstenergy= 1 > rlist= 0.8 > pbc = xyz > periodic_molecules = yes > coulombtype = user > rcoulomb = 0.8 > vdw-type = user > rvdw = 0.8 > constraints = none/ > > > I get following output: > > /Steepest Descents: >Tolerance (Fmax) = 1.0e+00 >Number of steps= 50 > Step=2, Dmax= 5.0e-04 nm, Epot= 4.40635e+11 Fmax= 8.77355e+10, atom= > 223 > Step=4, Dmax= 3.0e-04 nm, Epot= 4.40403e+11 Fmax= 9.61163e+10, atom= > 263 > Step=6, Dmax= 1.8e-04 nm, Epot= 4.40248e+11 Fmax= 1.01812e+11, atom= > 833 > Step=8, Dmax= 1.1e-04 nm, Epot= 4.40181e+11 Fmax= 9.36260e+10, atom= > 83 > Step= 10, Dmax= 6.5e-05 nm, Epot= 4.40142e+11 Fmax= 9.89456e+10, atom= > 833 > Step= 12, Dmax= 3.9e-05 nm, Epot= 4.40115e+11 Fmax= 8.24990e+10, atom= > 105 > Step= 14, Dmax= 2.3e-05 nm, Epot= 4.40094e+11 Fmax= 4.88140e+10, atom= > 105 > Step= 19, Dmax= 1.7e-06 nm, Epot= 4.40098e+11 Fmax= 4.47573e+10, atom= > 223 > Energy minimization has stopped, but the forces havenot converged to the > requested precision Fmax < 1 (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. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Back Off! I just backed up confout.gro to ./#confout.gro.4# > > Steepest Descents converged to machine precision in 20 steps, > but did not reach the requested Fmax < 1. > Potential Energy = 4.4009390e+11 > Maximum force = 4.8813974e+10 on atom 105 > Norm of force = 5.4008571e+09 > / > > I cannot recollect how energy minimisation output should look like - is > this > right? > > > It would be great to hear some suggestions how to pin-point t
[gmx-users] parallelization of processors on single system/node using MPI
Hi all, I'm working on a single server with 2 Intel Xeon E5-2660 processors. Each processor has 8C/16T, so total 16C/32T. I want to utilize both the processors for my simulation, thread MPI/ multithreading doesn't work as I'm doing calculations using plumed patch which supports the use of only 1 thread, resulting in a very poor performance. Can I use MPI with GROMACS-4.6.x version on single server/machine so that my simulation utilizes both the processors and the performance gets improved? if yes, please tell how can I do that? regards Richa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] step 0Segmentation fault: 11 (Mark Abraham)
Thank you, Mark. It makes sense. I am using FF developed by other group, that was run in Discover before. I am not sure I like how the plots of potentials look. V > > Huge forces lead to crazy displacements whose next forces are looked up > outside the boundaries of your table, which leads to a segmentation fault. > GROMACS doesn't waste its time checking for this, since that would hurt > everyone's performance and gain only a descriptive error that something is > horribly broken! > > Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] free energy landscape
Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham command to got the free energy landscapes. does it right or not? i have seen dihedral PCA from your website ( http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=landscape), should i use the g_covar and g_anaeig commands to get the free energy landscape with respect to Rg and RMSD? if yes, please tell how to do it , thank you very much! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
Define large fluctuations. They might be physical large fluctuations! On Thu, Nov 28, 2013 at 1:19 AM, bipin singh wrote: > Hello All, > > I am trying to calculate relative solvation free energy for p-Cresol and > p-Chlorophenol using Gromacs 4.6.3. > > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 > > During one transformation (lambda 0.0 to 1.0) I am switching off the vdW > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd > p-Chlorophenol respectively. > > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to 1.0) > for both the molecules. > > But I am getting a large fluctuation in dh/dl values only at initial lambda > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is > being changed to DUM). > > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I get > consistent values of dh/dl (i.e. less deviation during simulation). > > > Can anyone suggest the reason for this behaviour and how to select > appropriate values of sc-alpha based on transformation. And can we use > different sets of sc-alpha values for two molecules to compute their > relative solvation free energies. > > > > I have used the following mdp settings: > > sc-power = 1 > sc-alpha = 0.5 > sc-r-power = 6 > sc-coul = no > > > and > > > sc-power = 1 > sc-alpha = 0.0 > sc-r-power = 6 > sc-coul = no > > ### > > > > > > *Thanks and Regards,Bipin Singh* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] REMD on GPU
Dear Gromacs users! I'd like to perform replica exchange simulation For this I've made bash script which create n folders like replica-298 replica-312 replica-323 replica-334 ... replica-N with all files needed for simulation considted of specified mdp file with different ref_t value No I'd like to launch this simulation using -multidir replica-298 replica-312 replica-323 replica-334 Unfortunately I've obtained Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support Does it possible to install mpirun on the existing Gromacs-4.6 built from source (without removing of the installed files)? Does it possible to run replica simulations in GPU supported mode ? Thanks for help, James -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy landscape
On 11/28/13 7:20 AM, aixintiankong wrote: Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham command to got the free energy landscapes. does it right or not? i have seen dihedral PCA from your website ( Yes, that's correct. http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=landscape), should i use the g_covar and g_anaeig commands to get the free energy landscape with respect to Rg and RMSD? if yes, please tell how to do it , thank you very much! g_covar and g_anaeig are necessary in that case to extract the data of interest; those programs have no bearing on what you are doing. The process is identical though - generate a text file of the two variables of interest (for g_covar/g_anaeig, the columns are eigenvalues) and then plot with g_sham. -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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
Thanks for the reply. By large fluctuations, I mean the standard deviation of dh/dl values during the simulation at lambda 0.0 to 0.5 in comparison to lambda close to 1, when using sc-alpha=0.5 On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts wrote: > Define large fluctuations. They might be physical large fluctuations! > > > > On Thu, Nov 28, 2013 at 1:19 AM, bipin singh wrote: > > Hello All, > > > > I am trying to calculate relative solvation free energy for p-Cresol and > > p-Chlorophenol using Gromacs 4.6.3. > > > > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 > > > > During one transformation (lambda 0.0 to 1.0) I am switching off the vdW > > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd > > p-Chlorophenol respectively. > > > > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to > 1.0) > > for both the molecules. > > > > But I am getting a large fluctuation in dh/dl values only at initial > lambda > > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is > > being changed to DUM). > > > > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I > get > > consistent values of dh/dl (i.e. less deviation during simulation). > > > > > > Can anyone suggest the reason for this behaviour and how to select > > appropriate values of sc-alpha based on transformation. And can we use > > different sets of sc-alpha values for two molecules to compute their > > relative solvation free energies. > > > > > > > > I have used the following mdp settings: > > > > sc-power = 1 > > sc-alpha = 0.5 > > sc-r-power = 6 > > sc-coul = no > > > > > > and > > > > > > sc-power = 1 > > sc-alpha = 0.0 > > sc-r-power = 6 > > sc-coul = no > > > > ### > > > > > > > > > > > > *Thanks and Regards,Bipin Singh* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Thanks and Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: > Hi GMX Users, please help me > I am trying to begin a simulation of a protein and ligand coplex by > gromacs4.6.3. > > I am using AMBER99sb-ILDN force field and TIP4P water model. However, > I am facing a problem in the ion adding step. > > when I issue the grompp command to generate the necessary .tpr file > for simulation to be utilised by genion tool, I get the following > error : > > Fatal error: > number of coordinates in coordinate file (solv.gro, 102546) > does not match topology (topol.top, 133916) > > whe i use tip3p, i don't get error. > > Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] REMD on GPU
On Thu, Nov 28, 2013 at 3:01 PM, James Starlight wrote: > Dear Gromacs users! > > I'd like to perform replica exchange simulation > > For this I've made bash script which create n folders like > replica-298 > replica-312 > replica-323 > replica-334 > ... > replica-N > with all files needed for simulation considted of specified mdp file with > different ref_t value > No I'd like to launch this simulation using > -multidir replica-298 replica-312 replica-323 replica-334 > > Unfortunately I've obtained > > Fatal error: > mdrun -multi is not supported with the thread library.Please compile > GROMACS with MPI support > > Does it possible to install mpirun on the existing Gromacs-4.6 built from > source (without removing of the installed files)? > No, please compile GROMACS with MPI support, per the installation instructions. > Does it possible to run replica simulations in GPU supported mode ? > Yes, but you need to compile for both GPU and MPI. And see http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Using_multi-simulations_and_GPUs for mdrun tips. Mark Thanks for help, > > James > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] For GMX implicit solvent MD
Dear All, I'd like to do some implicit solvent MD with Gromacs. However, I meet a trouble. For instance, I have included gbsa.itp. when I used a SPC water molecule for Implicit Sovent MD，it goes very well. Then when I use two SPC water molecules，it give me a Fatal error: Fatal error: Death & horror! GB generic interaction not implemented. Can the GMX perform only a single molecule? What's wrong with my MD? Attachment: # cat water-spc.gro Protein 6 1SOL OW 1 0.502 0.516 0.052 -0.0106 -0.1291 -0.1474 1SOL HW1 2 0.432 0.548 -0.012 -0.9087 1.3904 1.5119 1SOL HW2 3 0.459 0.478 0.133 1.0765 0.6585 0.8283 2SOL OW 1 0.512 0.516 0.052 -0.0106 -0.1291 -0.1474 2SOL HW1 2 0.442 0.548 -0.012 -0.9087 1.3904 1.5119 2SOL HW2 3 0.469 0.478 0.133 1.0765 0.6585 0.8283 5.0 5.0 5.0 # cat prmd-is.mdp title = water cpp = /usr/bin/cpp define = -DPOSRES_ICE ;define = -DFLEXIBLE constraints = all-bonds integrator = md tinit = 0 dt = 0.002 ; ps ! nsteps = 2000 ; total 0.100 ns nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 10 nstcalcenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz;no coulombtype = cut-off; rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa gb_algorithm = OBC;HCT;Still nstgbradii = 1 rgbradii = 1.0 gb_epsilon_solvent = 80 gb_saltconc = 10 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 2.268 ;2.058/2.268 ; Temperature coupling is on in two groups Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 240 ; Pressure coupling is off Pcoupl = no;Berendsen; Parrinello-Rahman; MTTK; Isotropic; No pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = COM ; Generate velocites is on at 240 K. gen_vel = no gen_temp = 240.0 gen_seed = 173529 Your sincerely, -- Xiyuan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Maybe you should modify your .tpr file manually according to what you added in the previous sections! On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami < mahboobeh.esl...@yahoo.com> wrote: > dear timo > Please send me further details. I'm not a professional. > Thanks and regards > > > > > On Thursday, November 28, 2013 4:28 PM, Timo Graen wrote: > > On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: > > > Hi GMX Users, please help me > > I am trying to begin a simulation of a protein and ligand coplex by > gromacs4.6.3. > > > > I am using AMBER99sb-ILDN force field and TIP4P water model. However, > > I am facing a problem in the ion adding step. > > > > when I issue the grompp command to generate the necessary .tpr file > > for simulation to be utilised by genion tool, I get the following > > error : > > > > Fatal error: > > number of coordinates in coordinate file (solv.gro, 102546) > > does not match topology (topol.top, 133916) > > > > whe i use tip3p, i don't get error. > > > > Thank you very much > > Use share/gromacs/top/tip4p.gro when generating the simulation box, > tip4p has an aditional interaction site > > best > timo > > -- > -- > T.M.D. Graen > Max Planck Institute for Biophysical Chemistry > Theoretical and Computational Biophysics Department, 105 00 > Am Fassberg 11 > 37077 Goettingen, Germany > Tel.: ++49 551 201 2313 > Fax: ++49 551 201 2302 > Email: tgr...@gwdg.de > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file. I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks. -Justin On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami < mahboobeh.esl...@yahoo.com> wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] For GMX implicit solvent MD
On 11/28/13 9:31 AM, dxl...@hotmail.com wrote: Dear All, I'd like to do some implicit solvent MD with Gromacs. However, I meet a trouble. For instance, I have included gbsa.itp. when I used a SPC water molecule for Implicit Sovent MD，it goes very well. Then when I use two SPC water molecules，it give me a Fatal error: Fatal error: Death & horror! GB generic interaction not implemented. Can you please provide the full fatal error, including the referenced source file? Can the GMX perform only a single molecule? In theory it should be able to handle anything. What's wrong with my MD? Attachment: # cat water-spc.gro Protein 6 1SOL OW 1 0.502 0.516 0.052 -0.0106 -0.1291 -0.1474 1SOL HW1 2 0.432 0.548 -0.012 -0.9087 1.3904 1.5119 1SOL HW2 3 0.459 0.478 0.133 1.0765 0.6585 0.8283 2SOL OW 1 0.512 0.516 0.052 -0.0106 -0.1291 -0.1474 2SOL HW1 2 0.442 0.548 -0.012 -0.9087 1.3904 1.5119 2SOL HW2 3 0.469 0.478 0.133 1.0765 0.6585 0.8283 5.0 5.0 5.0 # cat prmd-is.mdp title = water cpp = /usr/bin/cpp define = -DPOSRES_ICE ;define = -DFLEXIBLE constraints = all-bonds integrator = md tinit = 0 dt = 0.002 ; ps ! nsteps = 2000 ; total 0.100 ns nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 10 nstcalcenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 pbc = xyz;no coulombtype = cut-off; rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.2 Note that finite cutoffs with PBC are a bad approach for running implicit solvent simulations. Use infinite cutoffs and no PBC. -Justin fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa gb_algorithm = OBC;HCT;Still nstgbradii = 1 rgbradii = 1.0 gb_epsilon_solvent = 80 gb_saltconc = 10 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 2.268 ;2.058/2.268 ; Temperature coupling is on in two groups Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 240 ; Pressure coupling is off Pcoupl = no;Berendsen; Parrinello-Rahman; MTTK; Isotropic; No pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = COM ; Generate velocites is on at 240 K. gen_vel = no gen_temp = 240.0 gen_seed = 173529 Your sincerely, -- Xiyuan -- == 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
I am mentioning below the average and standard deviation of dh/dl values at lambda=0.0 and lambda=1.0, for sc-alpha=0.5 Avg Std. lambda0.0-2.055812e+01 2.730571e+01 lambda1.07.086960e+017.670135e+00 On Thu, Nov 28, 2013 at 7:34 PM, bipin singh wrote: > Thanks for the reply. > > By large fluctuations, I mean the standard deviation of dh/dl values > during the simulation at lambda 0.0 to 0.5 in comparison to lambda close to > 1, when using sc-alpha=0.5 > > > On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts wrote: > >> Define large fluctuations. They might be physical large fluctuations! >> >> >> >> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh >> wrote: >> > Hello All, >> > >> > I am trying to calculate relative solvation free energy for p-Cresol and >> > p-Chlorophenol using Gromacs 4.6.3. >> > >> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 >> > >> > During one transformation (lambda 0.0 to 1.0) I am switching off the vdW >> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd >> > p-Chlorophenol respectively. >> > >> > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to >> 1.0) >> > for both the molecules. >> > >> > But I am getting a large fluctuation in dh/dl values only at initial >> lambda >> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is >> > being changed to DUM). >> > >> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I >> get >> > consistent values of dh/dl (i.e. less deviation during simulation). >> > >> > >> > Can anyone suggest the reason for this behaviour and how to select >> > appropriate values of sc-alpha based on transformation. And can we use >> > different sets of sc-alpha values for two molecules to compute their >> > relative solvation free energies. >> > >> > >> > >> > I have used the following mdp settings: >> > >> > sc-power = 1 >> > sc-alpha = 0.5 >> > sc-r-power = 6 >> > sc-coul = no >> > >> > >> > and >> > >> > >> > sc-power = 1 >> > sc-alpha = 0.0 >> > sc-r-power = 6 >> > sc-coul = no >> > >> > ### >> > >> > >> > >> > >> > >> > *Thanks and Regards,Bipin Singh* >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > > > -- > > > > *Thanks and Regards, Bipin Singh* > > -- *Thanks and Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] parallelization of processors on single system/node using MPI
Yes, you can besides the minor command-line interface differences, using MPI and thread-MPI works essentially the same way. http://www.gromacs.org/Documentation/Acceleration_and_parallelization#MPI.2c.c2.a0Thread-MPI -- Szilárd On Thu, Nov 28, 2013 at 11:07 AM, Richa Singh wrote: > Hi all, > > I'm working on a single server with 2 Intel Xeon E5-2660 > processors. Each processor has 8C/16T, so total 16C/32T. > > I want to utilize both the processors for my simulation, thread MPI/ > multithreading doesn't work as I'm doing calculations using plumed > patch which supports the use of only 1 thread, resulting in a very > poor performance. > > Can I use MPI with GROMACS-4.6.x version on single server/machine so > that my simulation utilizes both the processors and the performance > gets improved? > > if yes, please tell how can I do that? > > regards > Richa > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul wrote: > > > On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: > >> Maybe you should modify your .tpr file manually according to what you >> added >> in the previous sections! >> >> > Manually modify a .tpr? How would one do that? > > The OP needs to provide the exact commands issued. The fatal error shown > results from poor bookkeeping (i.e. not making use of the -p option of > genbox and genion) or use of the wrong water coordinate file. > > I would also suggest some basic tutorial material to become more familiar > with simple Gromacs tasks. > > -Justin > > > >> >> >> On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami < >> mahboobeh.esl...@yahoo.com> wrote: >> >> dear timo >>> Please send me further details. I'm not a professional. >>> Thanks and regards >>> >>> >>> >>> >>> On Thursday, November 28, 2013 4:28 PM, Timo Graen >>> wrote: >>> >>> On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: >>> >>> Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by >>> gromacs4.6.3. >>> I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much >>> >>> Use share/gromacs/top/tip4p.gro when generating the simulation box, >>> tip4p has an aditional interaction site >>> >>> best >>> timo >>> >>> -- >>> -- >>> T.M.D. Graen >>> Max Planck Institute for Biophysical Chemistry >>> Theoretical and Computational Biophysics Department, 105 00 >>> Am Fassberg 11 >>> 37077 Goettingen, Germany >>> Tel.: ++49 551 201 2313 >>> Fax: ++49 551 201 2302 >>> Email: tgr...@gwdg.de >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > 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 > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? Please let me know On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Oh, I am sorry, I made a big mistake! :) > > Best Regards > > > On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul wrote: > >> >> >> On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: >> >>> Maybe you should modify your .tpr file manually according to what you >>> added >>> in the previous sections! >>> >>> >> Manually modify a .tpr? How would one do that? >> >> The OP needs to provide the exact commands issued. The fatal error shown >> results from poor bookkeeping (i.e. not making use of the -p option of >> genbox and genion) or use of the wrong water coordinate file. >> >> I would also suggest some basic tutorial material to become more familiar >> with simple Gromacs tasks. >> >> -Justin >> >> >> >>> >>> >>> On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami < >>> mahboobeh.esl...@yahoo.com> wrote: >>> >>> dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me > I am trying to begin a simulation of a protein and ligand coplex by > gromacs4.6.3. > > I am using AMBER99sb-ILDN force field and TIP4P water model. However, > I am facing a problem in the ion adding step. > > when I issue the grompp command to generate the necessary .tpr file > for simulation to be utilised by genion tool, I get the following > error : > > Fatal error: > number of coordinates in coordinate file (solv.gro, 102546) > does not match topology (topol.top, 133916) > > whe i use tip3p, i don't get error. > > Thank you very much > Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> 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 >> >> == >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
It's very possible that this is entirely physical. dh/dl fluctuates a lot. You may want to look at graphs of after a few 10's of ps to see if it looks reasonable. On Thu, Nov 28, 2013 at 10:04 AM, bipin singh wrote: > I am mentioning below the average and standard deviation of dh/dl values at > lambda=0.0 and lambda=1.0, for sc-alpha=0.5 > > Avg Std. > lambda0.0-2.055812e+01 2.730571e+01 > > lambda1.07.086960e+017.670135e+00 > > > On Thu, Nov 28, 2013 at 7:34 PM, bipin singh wrote: > >> Thanks for the reply. >> >> By large fluctuations, I mean the standard deviation of dh/dl values >> during the simulation at lambda 0.0 to 0.5 in comparison to lambda close to >> 1, when using sc-alpha=0.5 >> >> >> On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts wrote: >> >>> Define large fluctuations. They might be physical large fluctuations! >>> >>> >>> >>> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh >>> wrote: >>> > Hello All, >>> > >>> > I am trying to calculate relative solvation free energy for p-Cresol and >>> > p-Chlorophenol using Gromacs 4.6.3. >>> > >>> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 >>> > >>> > During one transformation (lambda 0.0 to 1.0) I am switching off the vdW >>> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol amd >>> > p-Chlorophenol respectively. >>> > >>> > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to >>> 1.0) >>> > for both the molecules. >>> > >>> > But I am getting a large fluctuation in dh/dl values only at initial >>> lambda >>> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 is >>> > being changed to DUM). >>> > >>> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to 0.5), I >>> get >>> > consistent values of dh/dl (i.e. less deviation during simulation). >>> > >>> > >>> > Can anyone suggest the reason for this behaviour and how to select >>> > appropriate values of sc-alpha based on transformation. And can we use >>> > different sets of sc-alpha values for two molecules to compute their >>> > relative solvation free energies. >>> > >>> > >>> > >>> > I have used the following mdp settings: >>> > >>> > sc-power = 1 >>> > sc-alpha = 0.5 >>> > sc-r-power = 6 >>> > sc-coul = no >>> > >>> > >>> > and >>> > >>> > >>> > sc-power = 1 >>> > sc-alpha = 0.0 >>> > sc-r-power = 6 >>> > sc-coul = no >>> > >>> > ### >>> > >>> > >>> > >>> > >>> > >>> > *Thanks and Regards,Bipin Singh* >>> > -- >>> > Gromacs Users mailing list >>> > >>> > * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> > >>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > >>> > * For (un)subscribe requests visit >>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> >> >> >> -- >> >> >> >> *Thanks and Regards, Bipin Singh* >> >> > > > -- > > > > *Thanks and Regards,Bipin Singh* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER ff10 with Gromacs
In addition to where Szilard said to look, you can also try looking for force fields on the user contributions part of the GROMACS website: http://www.gromacs.org/Downloads/User_contributions/Force_fields If you need to use AMBER99SB force field with the ParmBSC0 nucleic acid parameters, this combination can be found there. Cheers Tom On 11/27/2013 02:06 PM, Szilárd Páll wrote: Hi, If you look at share/gromacs/top/ in the GROMACS installation directory you can see which FF-s are included and amberff10 is not there, so the answer is no. Cheers, -- Szilárd On Wed, Nov 27, 2013 at 12:33 AM, gromacs query wrote: Dear All I never used Gromacs for nucleic acids. In AMBER there is ff10 (ff99SB+parmbasco+ also one needs to add ions according to water used by Thomas Cheatham et al.) does gromacs include this force field (AMBER ff implemented in gromacs)? regards JIo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote: Dear Justin I meant modifying .top file after adding some ions and water molecules which could be equivalent to -p option as you mentioned. What do you think about this? That would be one possible solution, but it is not yet clear what the OP has done or failed to do correctly. One does not need to make manual modifications if -p has properly been used with genbox and genion. The fact that the coordinate file specifies fewer atoms than the topology suggests that perhaps the wrong water coordinates were used (e.g. a 3-point model instead of a 4-point model), as would happen if one follows tutorials too literally and specifies genbox -cs spc216.gro instead of -cs tip4p.gro. Many things could be wrong. The OP needs to provide more details so we can stop guessing and arrive at a solution. -Justin Please let me know On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file. I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks. -Justin On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami < mahboobeh.esl...@yahoo.com> wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards On Thursday, November 28, 2013 4:28 PM, Timo Graen wrote: On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: Hi GMX Users, please help me I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3. I am using AMBER99sb-ILDN force field and TIP4P water model. However, I am facing a problem in the ion adding step. when I issue the grompp command to generate the necessary .tpr file for simulation to be utilised by genion tool, I get the following error : Fatal error: number of coordinates in coordinate file (solv.gro, 102546) does not match topology (topol.top, 133916) whe i use tip3p, i don't get error. Thank you very much Use share/gromacs/top/tip4p.gro when generating the simulation box, tip4p has an aditional interaction site best timo -- -- T.M.D. Graen Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department, 105 00 Am Fassberg 11 37077 Goettingen, Germany Tel.: ++49 551 201 2313 Fax: ++49 551 201 2302 Email: tgr...@gwdg.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
i would use genbox -cp box.pdb -cs tip4p -p topol.top -o waterTip4p.pdb best timo On 11/28/2013 03:23 PM, Mahboobeh Eslami wrote: dear timo Please send me further details. I'm not a professional. Thanks and regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model
Thank you for your reply. In this case it is easier to use -p option instead of manual modification but both of them are possible. Of course In some cases we need to modify .top files manually (protein-drug complex system). Thanks again for information On Thu, Nov 28, 2013 at 6:53 PM, Justin Lemkul wrote: > > > On 11/28/13 10:13 AM, Mohsen Ramezanpour wrote: > >> Dear Justin >> I meant modifying .top file after adding some ions and water molecules >> which could be equivalent to -p option as you mentioned. >> What do you think about this? >> > > That would be one possible solution, but it is not yet clear what the OP > has done or failed to do correctly. One does not need to make manual > modifications if -p has properly been used with genbox and genion. The > fact that the coordinate file specifies fewer atoms than the topology > suggests that perhaps the wrong water coordinates were used (e.g. a 3-point > model instead of a 4-point model), as would happen if one follows tutorials > too literally and specifies genbox -cs spc216.gro instead of -cs tip4p.gro. > > Many things could be wrong. The OP needs to provide more details so we > can stop guessing and arrive at a solution. > > -Justin > > > Please let me know >> >> >> >> On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour < >> ramezanpour.moh...@gmail.com> wrote: >> >> Oh, I am sorry, I made a big mistake! :) >>> >>> Best Regards >>> >>> >>> On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul wrote: >>> >>> On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you > added > in the previous sections! > > > Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor bookkeeping (i.e. not making use of the -p option of genbox and genion) or use of the wrong water coordinate file. I would also suggest some basic tutorial material to become more familiar with simple Gromacs tasks. -Justin > > On Thu, Nov 28, 2013 at 5:53 PM, Mahboobeh Eslami < > mahboobeh.esl...@yahoo.com> wrote: > > dear timo > >> Please send me further details. I'm not a professional. >> Thanks and regards >> >> >> >> >> On Thursday, November 28, 2013 4:28 PM, Timo Graen >> wrote: >> >> On Thu 28 Nov 2013 01:22:16 PM CET, Mahboobeh Eslami wrote: >> >> Hi GMX Users, please help me >> >>> I am trying to begin a simulation of a protein and ligand coplex by >>> >>> gromacs4.6.3. >> >> >>> I am using AMBER99sb-ILDN force field and TIP4P water model. However, >>> I am facing a problem in the ion adding step. >>> >>> when I issue the grompp command to generate the necessary .tpr file >>> for simulation to be utilised by genion tool, I get the following >>> error : >>> >>> Fatal error: >>> number of coordinates in coordinate file (solv.gro, 102546) >>> does not match topology (topol.top, 133916) >>> >>> whe i use tip3p, i don't get error. >>> >>> Thank you very much >>> >>> >> Use share/gromacs/top/tip4p.gro when generating the simulation box, >> tip4p has an aditional interaction site >> >> best >> timo >> >> -- >> -- >> T.M.D. Graen >> Max Planck Institute for Biophysical Chemistry >> Theoretical and Computational Biophysics Department, 105 00 >> Am Fassberg 11 >> 37077 Goettingen, Germany >> Tel.: ++49 551 201 2313 >> Fax: ++49 551 201 2302 >> Email: tgr...@gwdg.de >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> >> -- == Justin A. Lemkul, Ph.D. 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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or se
Re: [gmx-users] AMBER ff10 with Gromacs
PS: googling AMBER FF10 + GROMACS does give (at least) one relevant result: http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d They may have something useful and may be willing to share (and it would certainly be useful to have it in the contrib FF section as well). Cheers, -- Szilárd On Thu, Nov 28, 2013 at 4:26 PM, Thomas Piggot wrote: > In addition to where Szilard said to look, you can also try looking for > force fields on the user contributions part of the GROMACS website: > > http://www.gromacs.org/Downloads/User_contributions/Force_fields > > If you need to use AMBER99SB force field with the ParmBSC0 nucleic acid > parameters, this combination can be found there. > > Cheers > > Tom > > > On 11/27/2013 02:06 PM, Szilárd Páll wrote: >> >> Hi, >> >> If you look at share/gromacs/top/ in the GROMACS installation >> directory you can see which FF-s are included and amberff10 is not >> there, so the answer is no. >> >> Cheers, >> -- >> Szilárd >> >> >> On Wed, Nov 27, 2013 at 12:33 AM, gromacs query >> wrote: >>> >>> Dear All >>> >>> I never used Gromacs for nucleic acids. In AMBER there is ff10 >>> (ff99SB+parmbasco+ also one needs to add ions according to water used by >>> Thomas Cheatham et al.) >>> >>> does gromacs include this force field (AMBER ff implemented in gromacs)? >>> >>> regards >>> JIo >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. > > > -- > Dr Thomas Piggot > University of Southampton, UK. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] AMBER ff10 with Gromacs
Hi, both links helped: http://www.gromacs.org/Downloads/User_contributions/Force_fields (for ff99sb and parmbsc0 but need to check for double stranded dna) and improved ions here: http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d (they used Cheatham ions with Gromacs, may need to modify itp file) Taken from above paper "The potassium (radius 1.705 Å and well depth 0.1936829 kcal mol) parameters optimized by Cheatham and co-workers" (I should have done homework rather! sorry) thanks JIo On Thu, Nov 28, 2013 at 4:05 PM, Szilárd Páll wrote: > PS: googling AMBER FF10 + GROMACS does give (at least) one relevant > result: http://pubs.rsc.org/en/Content/ArticlePDF/2013/CP/c2cp44100d > > They may have something useful and may be willing to share (and it > would certainly be useful to have it in the contrib FF section as > well). > > Cheers, > -- > Szilárd > > > On Thu, Nov 28, 2013 at 4:26 PM, Thomas Piggot > wrote: > > In addition to where Szilard said to look, you can also try looking for > > force fields on the user contributions part of the GROMACS website: > > > > http://www.gromacs.org/Downloads/User_contributions/Force_fields > > > > If you need to use AMBER99SB force field with the ParmBSC0 nucleic acid > > parameters, this combination can be found there. > > > > Cheers > > > > Tom > > > > > > On 11/27/2013 02:06 PM, Szilárd Páll wrote: > >> > >> Hi, > >> > >> If you look at share/gromacs/top/ in the GROMACS installation > >> directory you can see which FF-s are included and amberff10 is not > >> there, so the answer is no. > >> > >> Cheers, > >> -- > >> Szilárd > >> > >> > >> On Wed, Nov 27, 2013 at 12:33 AM, gromacs query > > >> wrote: > >>> > >>> Dear All > >>> > >>> I never used Gromacs for nucleic acids. In AMBER there is ff10 > >>> (ff99SB+parmbasco+ also one needs to add ions according to water used > by > >>> Thomas Cheatham et al.) > >>> > >>> does gromacs include this force field (AMBER ff implemented in > gromacs)? > >>> > >>> regards > >>> JIo > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > > Dr Thomas Piggot > > University of Southampton, UK. > > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a > > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
Thanks for you reply Prof. Shirts. I have plotted the dh/dl values (link mentioned below), but I am not sure whether the fluctuation is in acceptable range at lambda=0.0. Please have a look at the plot and let me know your thoughts. http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png On Thu, Nov 28, 2013 at 8:44 PM, Michael Shirts wrote: > It's very possible that this is entirely physical. dh/dl fluctuates a > lot. You may want to look at graphs of after a few 10's of ps > to see if it looks reasonable. > > On Thu, Nov 28, 2013 at 10:04 AM, bipin singh > wrote: > > I am mentioning below the average and standard deviation of dh/dl values > at > > lambda=0.0 and lambda=1.0, for sc-alpha=0.5 > > > > Avg Std. > > lambda0.0-2.055812e+01 2.730571e+01 > > > > lambda1.07.086960e+017.670135e+00 > > > > > > On Thu, Nov 28, 2013 at 7:34 PM, bipin singh > wrote: > > > >> Thanks for the reply. > >> > >> By large fluctuations, I mean the standard deviation of dh/dl values > >> during the simulation at lambda 0.0 to 0.5 in comparison to lambda > close to > >> 1, when using sc-alpha=0.5 > >> > >> > >> On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts >wrote: > >> > >>> Define large fluctuations. They might be physical large fluctuations! > >>> > >>> > >>> > >>> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh > >>> wrote: > >>> > Hello All, > >>> > > >>> > I am trying to calculate relative solvation free energy for p-Cresol > and > >>> > p-Chlorophenol using Gromacs 4.6.3. > >>> > > >>> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,, 1.0 > >>> > > >>> > During one transformation (lambda 0.0 to 1.0) I am switching off the > vdW > >>> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol > amd > >>> > p-Chlorophenol respectively. > >>> > > >>> > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to > >>> 1.0) > >>> > for both the molecules. > >>> > > >>> > But I am getting a large fluctuation in dh/dl values only at initial > >>> lambda > >>> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3 > is > >>> > being changed to DUM). > >>> > > >>> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to > 0.5), I > >>> get > >>> > consistent values of dh/dl (i.e. less deviation during simulation). > >>> > > >>> > > >>> > Can anyone suggest the reason for this behaviour and how to select > >>> > appropriate values of sc-alpha based on transformation. And can we > use > >>> > different sets of sc-alpha values for two molecules to compute their > >>> > relative solvation free energies. > >>> > > >>> > > >>> > > >>> > I have used the following mdp settings: > >>> > > >>> > sc-power = 1 > >>> > sc-alpha = 0.5 > >>> > sc-r-power = 6 > >>> > sc-coul = no > >>> > > >>> > > >>> > and > >>> > > >>> > > >>> > sc-power = 1 > >>> > sc-alpha = 0.0 > >>> > sc-r-power = 6 > >>> > sc-coul = no > >>> > > >>> > ### > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > *Thanks and Regards,Bipin Singh* > >>> > -- > >>> > Gromacs Users mailing list > >>> > > >>> > * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > > >>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > > >>> > * For (un)subscribe requests visit > >>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >> > >> > >> > >> -- > >> > >> > >> > >> *Thanks and Regards, Bipin Singh* > >> > >> > > > > > > -- > > > > > > > > *Thanks and Regards,Bipin Singh* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https:/
[gmx-users] Gemcitabine topolgy for OPLS
Hi, i´m trying to run a MD with Gemcitabine using OPLS /AA ff, to get the .itp, should i use topolgen , and then calculate the charges with gaussian ussing ChelpG charges, and replace it, i was wondering if this procedure is correct, algo i´m pretending , to study this molecule with a CNT, and a membrane channel, should i have extra considerations? , if anybody can help me thanks a lot -- View this message in context: http://gromacs.5086.x6.nabble.com/Gemcitabine-topolgy-for-OPLS-tp5012903.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun_mpi_d
Hi everybody i install gromacs 4.6.3 double precision and parallel what is the best correct command for mdrun_mpi_d on single machine with multiple processors (core=8) thanks for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] For GMX implicit solvent MD
Dear all， I have changed the is.mdp file as following, However, the same error still can't be removed. What can I do for the simulation? title = spc water cpp = /usr/bin/cpp ;define = -DFLEXIBLE constraints = all-bonds integrator = md tinit = 0 dt = 0.002 ; ps ! nsteps = 2000 ; nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 10 nstcalcenergy = 10 nstlist = 10 ns_type = grid rlist = 0 pbc = no coulombtype = cut-off; rcoulomb = 0 vdwtype = cut-off rvdw = 0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa gb_algorithm = OBC;HCT;Still nstgbradii = 1 rgbradii = 0 gb_epsilon_solvent = 80 gb_saltconc = 10 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation sa_surface_tension = 2.268 ;2.058/2.268 ; Temperature coupling is on in two groups Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 240 ; Pressure coupling is off Pcoupl = no;Berendsen; Parrinello-Rahman; MTTK; Isotropic; No pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = COM ; Generate velocites is on at 240 K. gen_vel = no gen_temp = 240.0 gen_seed = 173529 -- xiyuan P.I.,Laboratory of Computational Biology University of Shanghai for Science & Technology At 2013-11-28 22:46:28,"Justin Lemkul" wrote: > > >On 11/28/13 9:31 AM, dxl...@hotmail.com wrote: >> Dear All, >> I'd like to do some implicit solvent MD with Gromacs. However, I meet a trouble. For instance, I have included gbsa.itp. when I used a SPC water molecule for Implicit Sovent MD，it goes very well. Then when I use two SPC water molecules，it give me a Fatal error: >> Fatal error: >> Death & horror! GB generic interaction not implemented. >> > >Can you please provide the full fatal error, including the referenced source file? > >> Can the GMX perform only a single molecule? > >In theory it should be able to handle anything. > >> What's wrong with my MD? >> Attachment: >> # cat water-spc.gro >> Protein >> 6 >> 1SOL OW 1 0.502 0.516 0.052 -0.0106 -0.1291 -0.1474 >> 1SOL HW1 2 0.432 0.548 -0.012 -0.9087 1.3904 1.5119 >> 1SOL HW2 3 0.459 0.478 0.133 1.0765 0.6585 0.8283 >> 2SOL OW 1 0.512 0.516 0.052 -0.0106 -0.1291 -0.1474 >> 2SOL HW1 2 0.442 0.548 -0.012 -0.9087 1.3904 1.5119 >> 2SOL HW2 3 0.469 0.478 0.133 1.0765 0.6585 0.8283 >> 5.0 5.0 5.0 >> >> # cat prmd-is.mdp >> title = water >> cpp = /usr/bin/cpp >> define = -DPOSRES_ICE >> ;define = -DFLEXIBLE >> constraints = all-bonds >> integrator = md >> tinit = 0 >> dt = 0.002 ; ps ! >> nsteps = 2000 ; total 0.100 ns >> nstxout = 1000 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 100 >> nstenergy = 10 >> nstcalcenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> pbc = xyz;no >> coulombtype = cut-off; >> rcoulomb = 1.0 >> vdwtype = cut-off >> rvdw = 1.2 > >Note that finite cutoffs with PBC are a bad approach for running implicit >solvent simulations. Use infinite cutoffs and no PBC. > >-Justin > >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 6 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> ; IMPLICIT SOLVENT ALGORITHM >> implicit_solvent = gbsa >> gb_algorithm = OBC;HCT;Still >> nstgbradii = 1 >> rgbradii = 1.0 >> gb_epsilon_solvent = 80 >> gb_saltconc = 10 >> gb_obc_alpha = 1 >> gb_obc_beta = 0.8 >> gb_obc_gamma = 4.85 >> gb_dielectric_offset = 0.009 >> sa_algorithm = Ace-approximation >> sa_surface_tension = 2.268 ;2.058/2.268 >> ; Temperature coupling is on in two groups >> Tcoupl = v-rescale >> tau_t = 0.1 >> tc_grps = system >> ref_t = 240 >> ; Pressure coupling is off >> Pcoupl = no;Berendsen; Parrinello-Rahman; MTTK; Isotropic; No >> pcoupltype = isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> refcoord_scaling = COM >> ; Generate velocites is on at 240 K. >> gen_vel = no >> gen_temp = 240.0 >> gen_seed = 173529 >> >> >> Your sincerely, >> >> -- >> >> Xiyuan >> > >-- >== > >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 > >== >-- >Gromacs Users mailing list > >* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L
Re: [gmx-users] mdrun_mpi_d
Dear Eslami, Gromacs 4.6.3 can automatically take up all the cores. If you want to run gromacs across the nodes. Then you need to compile using MPI. Detailed instruction is available here http://www.gromacs.org/Documentation/Installation_Instructions. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Nov 29, 2013 at 3:27 AM, Mahboobeh Eslami < mahboobeh.esl...@yahoo.com> wrote: > Hi everybody > i install gromacs 4.6.3 double precision and parallel > what is the best correct command for mdrun_mpi_d on single machine with > multiple processors (core=8) > > > thanks for your help > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun_mpi_d
hi i installed openmpi and i set -DGMX_MPI=ON in cmake command. are these casesenough? thanks On Friday, November 29, 2013 7:59 AM, Chandan Choudhury wrote: Dear Eslami, Gromacs 4.6.3 can automatically take up all the cores. If you want to run gromacs across the nodes. Then you need to compile using MPI. Detailed instruction is available here http://www.gromacs.org/Documentation/Installation_Instructions. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Nov 29, 2013 at 3:27 AM, Mahboobeh Eslami wrote: Hi everybody >i install gromacs 4.6.3 double precision and parallel >what is the best correct command for mdrun_mpi_d on single machine with >multiple processors (core=8) > > >thanks for your help >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
