[gmx-users] choice of ΔQm Optimized Energy
Greetings everyone, I was looking at the parameter files of a ligand. I found four files of ligand under the same name but differences were there in ΔQm Optimized Energy -1556371.3071 kJ.mol-1 -0.525 0.429 -0.250 which one should I use for my ligand interaction studies? looking forward for your suggestions. -- 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] list of missing interactions
Dear Gromacs users I am doing free energy calculation of protein-ligand complex and getting again n again same error:- Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Dih. Rest. of 3 missing 1 Could anyone please suggest me how to solve this error? I have tried to use -nt 2 -pin on in order to avoid domain decomposition. Looking forward to hearing from you. Thanks and regards Sadaf -- 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] gmx distance error - invalid index with -f vs -s input file
Thanks so much for your response. I have visualized the cg_traj.gro using VMD and did not observe any issues. Additionally, I was able to use cg_traj.gro to calculate bond angles using the gmx angle command along with the relevant index file without any issues. It appears to be more of a specific issue with gmx distance rather than the .gro/.xtc file itself. One thing I am particularly intrigued by is why sending the .gro file using the -s flag works, while the -f does not? Thanks, Travis > Hello all, > > I am using gmx distance to extract bond distances from a set of 200 > coarse-grained polymer molecules (10 "atoms" each). I created an index file > pointing to all of the bonds, and ran the command as > > gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg > > However, I was getting an error message upon choosing which index group to > use. > > "Inconsistency in user input: Invalid index group references encountered > Group 'bonds'cannot be used in selections, because it contains negative > atom indices and/or references atoms not present (largest allowed atom > index is 0)." > it looks that there is something wrong in reading your cg_traj.gro file (probably similar to what you had before with xtc file). Did you try to visualize cg_traj.gro using VMD (for example). > Both the .gro and .ndx file contain the correct atom indices (1-2000). > Interestingly enough, when I sent the same .gro file to gmx distance using > the -s tag, I was able to correctly get the bond distance histogram (albeit > I do not believe it includes all time points from the trajectory). > > gro/xtc file contains mainly information on the coordinates of the particles in the system. All other information related the particles (types/connectivity/interaction parameters and so on) are in .tpr file. But this file contains also the starting structure of your simulation. Thus I suggest to check again structural file (gro and xtc) - As far as I understood gmx distance -f cg_traj.xtc -s *.tpr -n bonds.ndx -oh bondhist.xvg is not working. gmx dump could also helpit prints the information in tpr (and also xtc file) to a standard output in a readable format. Best regards Alessandra > Does anyone have any insight onto why switching from an input trajectory > (-f) to an input structure (-s) using the same .gro file would alleviate > the error above, or what could be causing that error when sending a > trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be > greatly appreciated. > > Thanks, > Travis Meyer, Ph.D. > INSPIRE Postdoctoral Fellow > Gormley Lab, Rutgers University Travis Meyer, Ph.D. INSPIRE Postdoctoral Fellow Gormley Lab, Rutgers University -- 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] T-REMD stalled - no trr files generated
Hi, I have a system containing a dimer totaling about 600 residues solvated with 32,000 water molecules. I have 72 replicas that are spread between 300 - 406 K. Each replica is running on 5 Intel Skylake 6140 cores. The simulations have been running for 14 hours and no trr files have been generated and the md logs have not moved past the "maximum allowed distance for charge groups involved in interactions" section. I have run quick trials with only 4 replicas that did successfully write trajectories and perform exchanges but the full 72 replica run never seems to get moving. Any thoughts? Thank you, Dan -- 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] Build polymers with pdb2gmx
Dear GMX users, I am new to polymer simulation and want to build a polymer system for Gromacs. I have followed Justin's instruction to make polyethylene by editing the rtp and hdb file. But I have a couple of questions regarding a larger polymer configuration: 1. The example system (polyethylene) only has one repeat unit, is there a way to define the number of repeat unit and then generate the PDB file? I am also wondering if there is a way to make the configuration with random torsion? I currently use Gaussview to copy and paste, and the initial PDB is just a linear chain. Like this...^^O^^O^^O^^ 2. Since the PDB file is straightly from Gaussview, the atom names in the file are all in basic form (C, H, O...), in order for the pdb2gmx to work, I have to manually match and replace them according to the .rtp file. For larger repeat unit, is there a better way to do this? Thanks for your help and suggestions. -- Shi Li Research Assistant, Ph.D. Candidate Department of Chemistry & Center for Applied Energy Research (CAER) University of Kentucky Email: sli...@g.uky.edu -- 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] How to calculate the number of ligand and water molecules around protein?
Hi all, I wanted to ask about the best way to calculate the number of ligand molecules and water molecules around my protein at certain cut-off. I have used gmx trjorder -nshell and gmx select -os. Both have given me different results, so I wanted to know if anyone has had any luck with either to an accurate degree? Any guidance will be much appreciated. Akash -- 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] (no subject)
for what reasons you request the largest force in your system smaller than such small value? On Fri, Jan 24, 2020 at 1:22 PM Sadaf Rani wrote: > Dear Gromacs users > I am running a free energy calculation of the protein-ligand complex. > During the energy minimization process, I am getting many jumps in steps as > below:- > > Step Time > 1050010500.0 > >Energies (kJ/mol) >Bond Restraint Pot. AngleProper Dih. Improper Dih. > 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02 > LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) > 6.81295e+037.12692e+043.37954e+05 -6.56537e+03 -2.70668e+06 >Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) > 4.78029e+035.32468e+003.32764e+00 -2.26802e+060.0e+00 > Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl >-2.69428e+040.0e+000.0e+002.78529e+03 -1.65404e+02 > dVrestraint/dl Constr. rmsd > 0.0e+002.71623e-06 > >Step Time > 1050110501.0 > >Step Time > 1050210502.0 > >Step Time > 1050310503.0 > >Step Time > 1050410504.0 > >Step Time > 1050510505.0 > >Step Time > 1050610506.0 > >Step Time > 1050710507.0 > >Step Time > 1050810508.0 > >Step Time > 1050910509.0 > >Step Time > 1051010510.0 > >Step Time > 1051110511.0 > > > Energy minimization has stopped, but the forces have not converged to the > requested precision Fmax < 10 (which may not be possible for your system). > It > stopped because the algorithm tried to make a new step whose size was too > small, or there was no change in the energy since last step. Either way, we > regard the minimization as converged to within the available machine > precision, given your starting configuration and EM parameters. > > Double precision normally gives you higher accuracy, but this is often not > needed for preparing to run molecular dynamics. > You might need to increase your constraint accuracy, or turn > off constraints altogether (set constraints = none in mdp file) > > Steepest Descents converged to machine precision in 10512 steps, > but did not reach the requested Fmax < 10. > Potential Energy = -2.2680185e+06 > Maximum force = 6.3521606e+02 on atom 4653 > Norm of force = 3.6713926e+00 > > Should I use double precision for energy minimization? > I need your suggestions, > please. > > Thanks > > Sadaf Rani > -- > 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] Fwd:
Energy minimization getting jumps Dear Gromacs users I am running a free energy calculation of the protein-ligand complex. During the energy minimization process, I am getting many jumps in steps as below:- Step Time 1050010500.0 Energies (kJ/mol) Bond Restraint Pot. AngleProper Dih. Improper Dih. 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 6.81295e+037.12692e+043.37954e+05 -6.56537e+03 -2.70668e+06 Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.78029e+035.32468e+003.32764e+00 -2.26802e+060.0e+00 Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -2.69428e+040.0e+000.0e+002.78529e+03 -1.65404e+02 dVrestraint/dl Constr. rmsd 0.0e+002.71623e-06 Step Time 1050110501.0 Step Time 1050210502.0 Step Time 1050310503.0 Step Time 1050410504.0 Step Time 1050510505.0 Step Time 1050610506.0 Step Time 1050710507.0 Step Time 1050810508.0 Step Time 1050910509.0 Step Time 1051010510.0 Step Time 1051110511.0 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 10512 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.2680185e+06 Maximum force = 6.3521606e+02 on atom 4653 Norm of force = 3.6713926e+00 Should I use double precision for energy minimization? I need your suggestions, please. Thanks Sadaf Rani -- 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] (no subject)
Dear Gromacs users I am running a free energy calculation of the protein-ligand complex. During the energy minimization process, I am getting many jumps in steps as below:- Step Time 1050010500.0 Energies (kJ/mol) Bond Restraint Pot. AngleProper Dih. Improper Dih. 1.20860e+031.65864e+004.67218e+031.83350e+041.87873e+02 LJ-14 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) 6.81295e+037.12692e+043.37954e+05 -6.56537e+03 -2.70668e+06 Coul. recip.Angle Rest. Dih. Rest. Potential Pres. DC (bar) 4.78029e+035.32468e+003.32764e+00 -2.26802e+060.0e+00 Pressure (bar)dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl -2.69428e+040.0e+000.0e+002.78529e+03 -1.65404e+02 dVrestraint/dl Constr. rmsd 0.0e+002.71623e-06 Step Time 1050110501.0 Step Time 1050210502.0 Step Time 1050310503.0 Step Time 1050410504.0 Step Time 1050510505.0 Step Time 1050610506.0 Step Time 1050710507.0 Step Time 1050810508.0 Step Time 1050910509.0 Step Time 1051010510.0 Step Time 1051110511.0 Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 10512 steps, but did not reach the requested Fmax < 10. Potential Energy = -2.2680185e+06 Maximum force = 6.3521606e+02 on atom 4653 Norm of force = 3.6713926e+00 Should I use double precision for energy minimization? I need your suggestions, please. Thanks Sadaf Rani -- 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] cannot load the xtc file (without PBC) to VMD
Hey again, sorry for the late reply. I meant, I didn't have the chance to do that since a .trr file after the simulation was not generated. All I had was the em.trr. Later, I solved the problem by using editconf. Thank you for your attention. On Tue, Jan 14, 2020 at 2:51 PM wrote: > I didn't get you. So your problem is solved using trr file or not? > - Message from Lalehan Ozalp - > Date: Tue, 14 Jan 2020 12:53:54 +0300 > From: Lalehan Ozalp > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD > To: gmx-us...@gromacs.org > > > Thank you, but I haven't tried with a trr file and actually the last .trr > > file I've produced is em.trr. > > Thanks, > > > > On Mon, Jan 13, 2020 at 5:40 PM wrote: > > > >> Hii > >> Have you tried with the .trr file? Try the same procedure with .trr > file. > >> Thanks > >> - Message from Lalehan Ozalp - > >> Date: Mon, 13 Jan 2020 13:35:01 +0300 > >> From: Lalehan Ozalp > >> Reply-To: gmx-us...@gromacs.org > >> Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD > >> To: gmx-us...@gromacs.org > >> > >> Dear all, I have a question regarding loading .xtc file (with no > periodic > >> boundary conditions) to VMD which I generated before. To this end, I had > >> used the command: > >> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol > >> -ur > >> compact -center > >> and selected *protein* for centering, and *system* for output. > >> However, when I load my corresponding gro file to VMD, and then loading > >> the > >> xtc file above, the following error occurs: > >> > >> ERROR) BaseMolecule: attempt to init atoms while structure building in > >> progress! > >> ERROR) Invalid number of atoms in file: 132259 > >> Info) Using plugin xtc for coordinates from file > >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc > >> ERROR) Incorrect number of atoms (132259) in > >> ERROR) coordinate file > >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc > >> ERROR) Mismatch between existing molecule or structure file atom count > >> and > >> coordinate or trajectory file atom count. > >> Info) Finished with coordinate file > >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc. > >> > >> This is especially strange since I carried out the same procedure > several > >> times before. Additionally, I have a parallel system (with an isoenzyme > >> of > >> the enzyme used here, with the same cofactor and the same ligand) and > the > >> same steps worked perfectly. As a side note, this happens when I load > xtc > >> file without PBC, while does not happen when I load xtc file in the > >> presence of PBC. > >> > >> Thank you so much in advance! > >> Lalehan > >> -- > >> 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 > >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > >> - End message from Lalehan Ozalp - > >> -- > >> 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 > > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > send a mail to gmx-users-requ...@gromacs.org. > > - End message from Lalehan Ozalp - > -- > 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] gmx distance error - invalid index with -f vs -s input file
Hi, see below On Thu, Jan 23, 2020 at 7:34 PM Travis Meyer wrote: > Hello all, > > I am using gmx distance to extract bond distances from a set of 200 > coarse-grained polymer molecules (10 "atoms" each). I created an index file > pointing to all of the bonds, and ran the command as > > gmx distance -f cg_traj.gro -n bonds.ndx -oh bondhist.xvg > > However, I was getting an error message upon choosing which index group to > use. > > "Inconsistency in user input: Invalid index group references encountered > Group 'bonds'cannot be used in selections, because it contains negative > atom indices and/or references atoms not present (largest allowed atom > index is 0)." > > it looks that there is something wrong in reading your cg_traj.gro file (probably similar to what you had before with xtc file). Did you try to visualize cg_traj.gro using VMD (for example). > Both the .gro and .ndx file contain the correct atom indices (1-2000). > Interestingly enough, when I sent the same .gro file to gmx distance using > the -s tag, I was able to correctly get the bond distance histogram (albeit > I do not believe it includes all time points from the trajectory). > > gro/xtc file contains mainly information on the coordinates of the particles in the system. All other information related the particles (types/connectivity/interaction parameters and so on) are in .tpr file. But this file contains also the starting structure of your simulation. Thus I suggest to check again structural file (gro and xtc) - As far as I understood gmx distance -f cg_traj.xtc -s *.tpr -n bonds.ndx -oh bondhist.xvg is not working. gmx dump could also help ( http://manual.gromacs.org/documentation/2019-current/onlinehelp/gmx-dump.html?highlight=dump) it prints the information in tpr (and also xtc file) to a standard output in a readable format. Best regards Alessandra > Does anyone have any insight onto why switching from an input trajectory > (-f) to an input structure (-s) using the same .gro file would alleviate > the error above, or what could be causing that error when sending a > trajectory? I am new to GROMACS/Molecular Dynamics, so any help would be > greatly appreciated. > > Thanks, > Travis Meyer, Ph.D. > INSPIRE Postdoctoral Fellow > Gormley Lab, Rutgers University > -- > 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.
