[gmx-users] pulling of ligand
Dear GMX user I am working on enzyme ligand complex and want to calculate pmf of the complex. I have successfully energy minimized and equilibrated the system. But when I pull the ligand from the complex using the md_pull.mdp file then instead of ligand the protein is come out of the system. I have tried my best to solve the problem but not succeed. In the md_pull.mdp file I have given 1 for ligand and 0 for protein. If you kindly help me in this respect I will be very thankful to you. And your help will be highly appreciated. regards Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Centre of mass removal in CGMD
Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the centre of mass removal component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Units of k1 in the pulling code
Date: Thu, 12 Aug 2010 17:33:09 -0400 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] Units of k1 in the pulling code Dear Xueming: the word mol is short form for mole http://en.wikipedia.org/wiki/Mole_%28unit%29 In the pull code context, it refers to moles of the pulled group. The force is not applied to the COM of a cluster. The magnitude of the force is determined based on the COM distance, and then the force is applied to each atom in the pull groups. To clarify this, the force on the COM is not simply applied to each atom, but each atom receives a fraction of the COM force proportional to the mass of the atom divided by the mass of the whole COM group. Berk Chris. -- original message -- Hi there The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a cluster, the /mol in the units of force means per atom in the cluster, or single molecule composed of several atoms? Sorry, I don't know the default value of mol in gromacs. Does that mean per molecule? Besides, the force is applied to the COM of cluster, but in the real pulling process, the force is applied to each of the molecule in the cluster, or each of the atom in the cluster? Thanks in advance! Best! Xueming -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella histograms
Dear Chris Thanks but I am not using periodic boundary conditions as I want to simulate the two molecules in a vacuum. Gavin chris.ne...@utoronto.ca wrote: Dear Gavin: plot the position vs. time. Probably you will see it sample around one value, then discover a new state, and make a sharp transition to another value. If the new state is much more favourable than the initial state, then you can discard the initial state as equilibration. It might not be though... Also, could you have a PBC problem? I suggest that you read up on pull_pbcmol and try some tests with smart values of pull_pbcmol. Chris. -- original message -- Hi all I am generating a potential of mean force curve for the interaction between two cage molecules using umbrella sampling. The system is composed of only the two molecules in question, using no pbc and no cut-offs. Umbrella sampling is performed at 25 different distances (between COMs) between 0.75 and 2.75 nm. The histogram generated form g_wham shows very good overlap between the histogram between 0.75 nm and 2 nm. The shapes of the histogram and the width of the distribution are all well in this region. Above 2nm the histograms show two peaks and therefore the shape and distribution at these distances is poor. Has anyone ever come across this sort of behaviour before? Also can you use different force constants for the harmonic potential at different distances ? Cheers Gavin p.s Here is a copy of the mdp file that I am using title = Pull test cpp = include = define = integrator = md nsteps = 5000 dt = 0.002 nstxout = 25 nstvout = 25 nstlog = 25 nstenergy = 5000 nstfout = 25 pbc = no nstlist = 10 ns_type = simple vdwtype = cut-off rlist = 0 rvdw_switch = 0 rvdw= 0 coulombtype = cut-off rcoulomb= 0 tcoupl = nose-hoover tc_grps = system tau_t = 0.1 ref_t = 600 gen_vel = no gen_temp= constraints = none comm_mode = angular pull= umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_init1 = 2.59 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Centre of mass removal in CGMD
On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the centre of mass removal component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - This is the way to go :)) Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Centre of mass removal in CGMD
Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole x.peri...@rug.nl wrote: On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the centre of mass removal component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - This is the way to go :)) Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Centre of mass removal in CGMD
On Aug 13, 2010, at 12:37 PM, Anirban Ghosh wrote: Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? I guess so :)) Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole x.peri...@rug.nl wrote: On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the centre of mass removal component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation: - ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W - This is the way to go :)) Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pulling of ligand
abdul wadood wrote: Dear GMX user I am working on enzyme ligand complex and want to calculate pmf of the complex. I have successfully energy minimized and equilibrated the system. But when I pull the ligand from the complex using the md_pull.mdp file then instead of ligand the protein is come out of the system. Sounds like a normal consequence of periodic boundary conditions. See FAQ #11: http://www.gromacs.org/Documentation/FAQs -Justin I have tried my best to solve the problem but not succeed. In the md_pull.mdp file I have given 1 for ligand and 0 for protein. If you kindly help me in this respect I will be very thankful to you. And your help will be highly appreciated. regards Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Re: Segmantation fault at g_traj
Jorge Alberto Jover Galtier wrote: Hi, Justin. Thank you for answering so quickly. We write you directly because we receive the daily digest from Gromacs and we are not sure how to answer to the thread. We have tried what you suggested, using 10,000 steps and Reply to the message, strip out any unnecessary posts in the digest, and change the subject line back to what you originally set it as (i.e., not gmx-users digest...). I must insist that you keep all correspondence on the list so that others can benefit from the conversation, and hopefully help out if necessary. writing data every 100 steps, and we still have the same problem. The protein we are using is a very small one, with 59 atoms, and we are working in vacuum. What about my suggestion for using g_traj -b and/or -e to write just a few frames? This would be a far more useful test. The only idea we have is that maybe we are making some mistakes at generating the .gro and .top files. These are the instructions we are using. From the .pdb file, we use: Your problem is from an analysis tool, not from any of these files. Your simulation successfully ran, but your analysis broke down. The only file worth checking would be the .trr file (using gmxcheck), in case it was corrupted during the run. pdb2gmx -ignh -f pep.pdb -o pep.gro -p pep.top We use the default force field and water model. And then we create the box to the protein: editconf -f pep.gro -d 0.7 -o pep_ini.gro After that, we begin the simulations. We send you the files we are working with, in case you want to try something. And if you have some I don't have the means or reason to re-run your system from the start. As I said, the problem is with an analysis tool, not the run itself. If g_traj is still failing, please post a complete description of your hardware, compilers, etc including all of the following: 1. Gromacs version 2. Compilers used (version is especially important) 3. Installation commands (configuration) 4. Hardware and OS -Justin other ideas, we would be really pleased to read them. Thank you very much in advance and best wishes, Jorge Alberto Jover Galtier Universidad de Zaragoza, Spain Anuncia tu coche Gratis con AutoScout24 http://addoubleclick.net/clk;227212367;7031886;i?http://www.autoscout24.es/QuickSearch.aspx?extcidm=7628a0308201490 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] the mdrun choked or maybe braked.
Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge group borders and 43271 shake borders There are 43271 total borders Division over nodes in atoms: 9348934893489351934893519348935193489351 9348935193489350 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 3245, targetcg=25208, myshift=8 CPU= 1, lastcg= 6361, targetcg=28324, myshift=8 CPU= 2, lastcg= 9477, targetcg=31440, myshift=8 CPU= 3, lastcg=12594, targetcg=34557, myshift=8 CPU= 4, lastcg=15710, targetcg=37673, myshift=8 CPU= 5, lastcg=18827, targetcg=40790, myshift=8 CPU= 6, lastcg=21943, targetcg=43906, myshift=7 CPU= 7, lastcg=25060, targetcg= 3098, myshift=7 CPU= 8, lastcg=28176, targetcg= 6214, myshift=7 CPU= 9, lastcg=31293, targetcg= 9331, myshift=7 CPU= 10, lastcg=34409, targetcg=12447, myshift=7 CPU= 11, lastcg=37526, targetcg=15564, myshift=7 CPU= 12, lastcg=40642, targetcg=18680, myshift=7 CPU= 13, lastcg=43924, targetcg=21962, myshift=8 pd-shift = 8, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 8 910 111213 G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0 0 0 0 PDIHS 774 0 0 0 0 0 0 0 0 0 0 0 0 0 IDIHS 852 0 0 0 0 0 0 0 0 0 0 0 0 0 LJ14 2436 0 0 0 0 0 0 0 0 0 0 0 0 0 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 3116 3116 3117 3116 3117 3116 3117 3116 3117 3116 3117 3116 3034 Workload division nnodes: 14 pd-shift:8 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 40643 3282 Max number of connections per atom is 27 Total number of connections is 32076 Max number of graph edges per atom is 4 Total number of graph edges is 13572 Initial temperature: 303.113 K Started mdrun on node 0 Fri Aug 13 14:38:46 2010 Step Time Lambda 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+01 Cons. rmsd () 2.63140e-05 Nothing more at the end, I changed the 16 cores to 14 cores, still has the same problem. And when I checked the status, it showed me it's finished. Thanks for any advice, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] the mdrun choked or maybe braked.
#ZHAO LINA# wrote: Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge group borders and 43271 shake borders There are 43271 total borders Division over nodes in atoms: 93489348934893519348935193489351 93489351 9348935193489350 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 3245, targetcg=25208, myshift=8 CPU= 1, lastcg= 6361, targetcg=28324, myshift=8 CPU= 2, lastcg= 9477, targetcg=31440, myshift=8 CPU= 3, lastcg=12594, targetcg=34557, myshift=8 CPU= 4, lastcg=15710, targetcg=37673, myshift=8 CPU= 5, lastcg=18827, targetcg=40790, myshift=8 CPU= 6, lastcg=21943, targetcg=43906, myshift=7 CPU= 7, lastcg=25060, targetcg= 3098, myshift=7 CPU= 8, lastcg=28176, targetcg= 6214, myshift=7 CPU= 9, lastcg=31293, targetcg= 9331, myshift=7 CPU= 10, lastcg=34409, targetcg=12447, myshift=7 CPU= 11, lastcg=37526, targetcg=15564, myshift=7 CPU= 12, lastcg=40642, targetcg=18680, myshift=7 CPU= 13, lastcg=43924, targetcg=21962, myshift=8 pd-shift = 8, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 8 910 111213 G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0 0 0 0 PDIHS 774 0 0 0 0 0 0 0 0 0 0 0 0 0 IDIHS 852 0 0 0 0 0 0 0 0 0 0 0 0 0 LJ14 2436 0 0 0 0 0 0 0 0 0 0 0 0 0 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 3116 3116 3117 3116 3117 3116 3117 3116 3117 3116 3117 3116 3034 Workload division nnodes: 14 pd-shift:8 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 40643 3282 Max number of connections per atom is 27 Total number of connections is 32076 Max number of graph edges per atom is 4 Total number of graph edges is 13572 Initial temperature: 303.113 K Started mdrun on node 0 Fri Aug 13 14:38:46 2010 Step Time Lambda 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+01 Cons. rmsd () 2.63140e-05 Nothing more at the end, I changed the 16 cores to 14 cores, still has the same problem. And when I checked the status, it showed me it's finished. Please provide more information. It mdrun stopped, it must have had a reason. Please provide your .mdp file, description of the system, and what you did as far as energy minimization and/or equilibration prior to whatever this run was doing. If mdrun fails, there's always a reason, and it would be very odd if Gromacs simply stopped without providing some kind of indicative output. -Justin Thanks for any advice, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post?
RE: [gmx-users] the mdrun choked or maybe braked.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, August 13, 2010 7:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdrun choked or maybe braked. #ZHAO LINA# wrote: Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge group borders and 43271 shake borders There are 43271 total borders Division over nodes in atoms: 93489348934893519348935193489351 93489351 9348935193489350 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 3245, targetcg=25208, myshift=8 CPU= 1, lastcg= 6361, targetcg=28324, myshift=8 CPU= 2, lastcg= 9477, targetcg=31440, myshift=8 CPU= 3, lastcg=12594, targetcg=34557, myshift=8 CPU= 4, lastcg=15710, targetcg=37673, myshift=8 CPU= 5, lastcg=18827, targetcg=40790, myshift=8 CPU= 6, lastcg=21943, targetcg=43906, myshift=7 CPU= 7, lastcg=25060, targetcg= 3098, myshift=7 CPU= 8, lastcg=28176, targetcg= 6214, myshift=7 CPU= 9, lastcg=31293, targetcg= 9331, myshift=7 CPU= 10, lastcg=34409, targetcg=12447, myshift=7 CPU= 11, lastcg=37526, targetcg=15564, myshift=7 CPU= 12, lastcg=40642, targetcg=18680, myshift=7 CPU= 13, lastcg=43924, targetcg=21962, myshift=8 pd-shift = 8, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 8 910 111213 G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0 0 0 0 PDIHS 774 0 0 0 0 0 0 0 0 0 0 0 0 0 IDIHS 852 0 0 0 0 0 0 0 0 0 0 0 0 0 LJ14 2436 0 0 0 0 0 0 0 0 0 0 0 0 0 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 3116 3116 3117 3116 3117 3116 3117 3116 3117 3116 3117 3116 3034 Workload division nnodes: 14 pd-shift:8 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 40643 3282 Max number of connections per atom is 27 Total number of connections is 32076 Max number of graph edges per atom is 4 Total number of graph edges is 13572 Initial temperature: 303.113 K Started mdrun on node 0 Fri Aug 13 14:38:46 2010 Step Time Lambda 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+01 Cons. rmsd () 2.63140e-05 Nothing more at the end, I changed the 16 cores to 14 cores, still has the same problem. And when I checked the status, it showed me it's finished. Please provide more information. It mdrun stopped, it must have had a reason. Please provide your .mdp file, description of the system, and what you did as far as energy minimization and/or equilibration prior to whatever this run was doing. If mdrun fails, there's always a reason, and it would be very odd if Gromacs simply stopped without providing some kind of indicative output. -Justin Can you tell me the possible reasons? Mainly which part I need to check? Thanks, lina -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use
Re: [gmx-users] the mdrun choked or maybe braked.
#ZHAO LINA# wrote: From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, August 13, 2010 7:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdrun choked or maybe braked. #ZHAO LINA# wrote: Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge group borders and 43271 shake borders There are 43271 total borders Division over nodes in atoms: 93489348934893519348935193489351 93489351 9348935193489350 Walking down the molecule graph to make constraint-blocks CPU= 0, lastcg= 3245, targetcg=25208, myshift=8 CPU= 1, lastcg= 6361, targetcg=28324, myshift=8 CPU= 2, lastcg= 9477, targetcg=31440, myshift=8 CPU= 3, lastcg=12594, targetcg=34557, myshift=8 CPU= 4, lastcg=15710, targetcg=37673, myshift=8 CPU= 5, lastcg=18827, targetcg=40790, myshift=8 CPU= 6, lastcg=21943, targetcg=43906, myshift=7 CPU= 7, lastcg=25060, targetcg= 3098, myshift=7 CPU= 8, lastcg=28176, targetcg= 6214, myshift=7 CPU= 9, lastcg=31293, targetcg= 9331, myshift=7 CPU= 10, lastcg=34409, targetcg=12447, myshift=7 CPU= 11, lastcg=37526, targetcg=15564, myshift=7 CPU= 12, lastcg=40642, targetcg=18680, myshift=7 CPU= 13, lastcg=43924, targetcg=21962, myshift=8 pd-shift = 8, pd-bshift= 0 Division of bonded forces over processors CPU 0 1 2 3 4 5 6 7 8 910 111213 G96ANGLES 2376 0 0 0 0 0 0 0 0 0 0 0 0 0 PDIHS 774 0 0 0 0 0 0 0 0 0 0 0 0 0 IDIHS 852 0 0 0 0 0 0 0 0 0 0 0 0 0 LJ14 2436 0 0 0 0 0 0 0 0 0 0 0 0 0 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 3116 3116 3117 3116 3117 3116 3117 3116 3117 3116 3117 3116 3034 Workload division nnodes: 14 pd-shift:8 pd-bshift: 0 Nodeid atom0 #atom cg0 #cg 0 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 40643 3282 Max number of connections per atom is 27 Total number of connections is 32076 Max number of graph edges per atom is 4 Total number of graph edges is 13572 Initial temperature: 303.113 K Started mdrun on node 0 Fri Aug 13 14:38:46 2010 Step Time Lambda 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+04 LJ (SR)LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+01 Cons. rmsd () 2.63140e-05 Nothing more at the end, I changed the 16 cores to 14 cores, still has the same problem. And when I checked the status, it showed me it's finished. Please provide more information. It mdrun stopped, it must have had a reason. Please provide your .mdp file, description of the system, and what you did as far as energy minimization and/or equilibration prior to whatever this run was doing. If mdrun fails, there's always a reason, and it would be very odd if Gromacs simply stopped without providing some kind of indicative output. -Justin Can you tell me the possible reasons? Mainly which part I need to check? Based on what you posted before, there is no possible way to tell you what's wrong, and hence why I asked for more information. Check all output - stdout, stderr, log files, whatever other files your queuing system (if applicable) might give you. There are numerous reasons for mdrun to stop, but very odd that
[gmx-users] Question about g_hbond output
Hi evergyone, I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running g_hbond -s md.tpr -f md.xtc -num numhbond.xvg There are 3 columns in the output files. The first column = frame The second column = H bonds The third column = pairs within 0.35nm The third column value is the number of all pairs with 0.35nm including the H bonds, but why the value is less than the second column value (the number of H bonds). This is my output of g_hbond. @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 2000 1 0 2000.5 1 0 2001 1 0 2001.5 1 0 2002 1 0 2002.5 1 0 2003 1 1 2003.5 1 0 2004 1 0 2004.5 1 1 2005 1 0 2005.5 1 0 2006 1 0 2006.5 1 0 2007 1 1 2007.5 2 0 2008 1 0 2008.5 1 0 Jinyao Wang wan...@ciac.jl.cn 2010-08-13 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about g_hbond output
Jinyao Wang wrote: Hi evergyone, I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running g_hbond -s md.tpr -f md.xtc -num numhbond.xvg There are 3 columns in the output files. The first column = frame The second column = H bonds The third column = pairs within 0.35nm The third column value is the number of all pairs with 0.35nm including the H bonds, but why the value is less than the second column value (the number of H bonds). Your interpretation of the column is wrong: http://lists.gromacs.org/pipermail/gmx-users/2010-March/049505.html -Justin This is my output of g_hbond. @title Hydrogen Bonds @xaxis label Time @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 2000 1 0 2000.5 1 0 2001 1 0 2001.5 1 0 2002 1 0 2002.5 1 0 2003 1 1 2003.5 1 0 2004 1 0 2004.5 1 1 2005 1 0 2005.5 1 0 2006 1 0 2006.5 1 0 2007 1 1 2007.5 2 0 2008 1 0 2008.5 1 0 Jinyao Wang wan...@ciac.jl.cn 2010-08-13 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ener.edr
Hello, Does gromacs write the current values (at some requested step) to ENER.EDR or the averaged ones (at the requested interval)? -- Dr. Vitaly Chaban Associate Researcher Department of Chemistry University of Roshester, Rochester, NY 14642 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] editconf
Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o)Run editconf to define the box (editconf -d 1)run gromp and mdrun for the minimizationRun editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? Thank you in advance, Abdullah -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ener.edr
The .edr file contains the instantaneous energies at every nstenergy steps. -- original message -- Hello, Does gromacs write the current values (at some requested step) to ENER.EDR or the averaged ones (at the requested interval)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf
abdullah ahmed wrote: Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) 2. Run editconf to define the box (editconf -d 1) 3. run gromp and mdrun for the minimization 4. Run editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? What is it exactly that you're seeing? The output .gro file from mdrun (which can be output as .pdb directly, if you prefer) contains only coordinates and box vectors, so anything else should just be comment lines. -Justin Thank you in advance, Abdullah -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf
-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul jalem...@vt.edu wrote: abdullah ahmed wrote: Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) 2. Run editconf to define the box (editconf -d 1) 3. run gromp and mdrun for the minimization use mdrun -c . It will give you the required pdb file Chandan 4. Run editconf to re-convert back to pdb Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? What is it exactly that you're seeing? The output .gro file from mdrun (which can be output as .pdb directly, if you prefer) contains only coordinates and box vectors, so anything else should just be comment lines. -Justin Thank you in advance, Abdullah -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] ener.edr
To be more precise, it writes both the current values and the sum over the steps to let g_energy print exact averages. Berk Date: Fri, 13 Aug 2010 11:08:24 -0400 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] ener.edr The .edr file contains the instantaneous energies at every nstenergy steps. -- original message -- Hello, Does gromacs write the current values (at some requested step) to ENER.EDR or the averaged ones (at the requested interval)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella histograms
Dear Chris In relation to the correspondence below, I should've mentioned that the peaks are symmetrical about the equilibrium distance as supposed to the there being one main peak at the equilibrium distance. Also should there be much of difference if you set pull_init to equal the distance between the COMs from the initial configuration, or if you set the value in the mdp file (which may be slightly different from that of the initial configuration). When I set pull_init to equal the that of the initial configuration i.e.pull_init =0 and pull_start = yes, there is much less fluctuation about the equilibrium distance than if I set pull_init to a value that is close to that of the initial configuration. (note all other parameters are the same) Gavin chris.ne...@utoronto.ca wrote: Dear Gavin: plot the position vs. time. Probably you will see it sample around one value, then discover a new state, and make a sharp transition to another value. If the new state is much more favourable than the initial state, then you can discard the initial state as equilibration. It might not be though... Also, could you have a PBC problem? I suggest that you read up on pull_pbcmol and try some tests with smart values of pull_pbcmol. Chris. -- original message -- Hi all I am generating a potential of mean force curve for the interaction between two cage molecules using umbrella sampling. The system is composed of only the two molecules in question, using no pbc and no cut-offs. Umbrella sampling is performed at 25 different distances (between COMs) between 0.75 and 2.75 nm. The histogram generated form g_wham shows very good overlap between the histogram between 0.75 nm and 2 nm. The shapes of the histogram and the width of the distribution are all well in this region. Above 2nm the histograms show two peaks and therefore the shape and distribution at these distances is poor. Has anyone ever come across this sort of behaviour before? Also can you use different force constants for the harmonic potential at different distances ? Cheers Gavin p.s Here is a copy of the mdp file that I am using title = Pull test cpp = include = define = integrator = md nsteps = 5000 dt = 0.002 nstxout = 25 nstvout = 25 nstlog = 25 nstenergy = 5000 nstfout = 25 pbc = no nstlist = 10 ns_type = simple vdwtype = cut-off rlist = 0 rvdw_switch = 0 rvdw= 0 coulombtype = cut-off rcoulomb= 0 tcoupl = nose-hoover tc_grps = system tau_t = 0.1 ref_t = 600 gen_vel = no gen_temp= constraints = none comm_mode = angular pull= umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = no pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_init1 = 2.59 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 1000 pull_nstfout = 1000 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: ener.edr
Berk, if I need the average values between 0...N, N...2N, etc - what is the convenient way to get them automatically (in energy.xvg)? Thank you, Vitaly To be more precise, it writes both the current values and the sum over the steps to let g_energy print exact averages. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella histograms
As I said before, please plot the position vs. time. It would be best if you can make a graph of this and post it to some web tool. I use photobucket, but there are many others. I realize that you think you are starting at equilibrium, but there are always things that can have unexpected consequences, not the least of which is: ref_t = 600 gen_vel = no Chris. -- original message -- Dear Chris In relation to the correspondence below, I should've mentioned that the peaks are symmetrical about the equilibrium distance as supposed to the there being one main peak at the equilibrium distance. Also should there be much of difference if you set pull_init to equal the distance between the COMs from the initial configuration, or if you set the value in the mdp file (which may be slightly different from that of the initial configuration). When I set pull_init to equal the that of the initial configuration i.e.pull_init =0 and pull_start = yes, there is much less fluctuation about the equilibrium distance than if I set pull_init to a value that is close to that of the initial configuration. (note all other parameters are the same) Gavin chris.neale at utoronto.ca wrote: Dear Gavin: plot the position vs. time. Probably you will see it sample around one value, then discover a new state, and make a sharp transition to another value. If the new state is much more favourable than the initial state, then you can discard the initial state as equilibration. It might not be though... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RE: ener.edr
In version 4.0 g_energy -aver prints the sum up till time t. You then have to subtract the value at the previous step and divide by the number of steps between frames. You can also download 4.5-beta, there g_energy -aver will directly print the averages over the last -nstenergy steps, also of edr files generated with 4.0. Berk From: vvcha...@gmail.com Date: Fri, 13 Aug 2010 18:35:34 +0300 To: g...@hotmail.com; gmx-users@gromacs.org CC: Subject: [gmx-users] RE: ener.edr Berk, if I need the average values between 0...N, N...2N, etc - what is the convenient way to get them automatically (in energy.xvg)? Thank you, Vitaly To be more precise, it writes both the current values and the sum over the steps to let g_energy print exact averages. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella histograms
Thanks Chris I have equilibrated the system at 600 K in a previous run therefore would it not be equilibrated, and also would the velocities from the final configuration of the equilibration not be sufficient as equilibrium velocities going into the main simulation Gavin chris.ne...@utoronto.ca wrote: As I said before, please plot the position vs. time. It would be best if you can make a graph of this and post it to some web tool. I use photobucket, but there are many others. I realize that you think you are starting at equilibrium, but there are always things that can have unexpected consequences, not the least of which is: ref_t = 600 gen_vel = no Chris. -- original message -- Dear Chris In relation to the correspondence below, I should've mentioned that the peaks are symmetrical about the equilibrium distance as supposed to the there being one main peak at the equilibrium distance. Also should there be much of difference if you set pull_init to equal the distance between the COMs from the initial configuration, or if you set the value in the mdp file (which may be slightly different from that of the initial configuration). When I set pull_init to equal the that of the initial configuration i.e.pull_init =0 and pull_start = yes, there is much less fluctuation about the equilibrium distance than if I set pull_init to a value that is close to that of the initial configuration. (note all other parameters are the same) Gavin chris.neale at utoronto.ca wrote: Dear Gavin: plot the position vs. time. Probably you will see it sample around one value, then discover a new state, and make a sharp transition to another value. If the new state is much more favourable than the initial state, then you can discard the initial state as equilibration. It might not be though... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella histograms
Gavin, I wish you the best of luck. Perhaps somebody else on the list can help you. -- original message -- Thanks Chris I have equilibrated the system at 600 K in a previous run therefore would it not be equilibrated, and also would the velocities from the final configuration of the equilibration not be sufficient as equilibrium velocities going into the main simulation Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] umbrella histograms
Chris Cheers and thanks for the suggestions. P.S. I hope you don't think that the previous msg was in anyway rude. It was actually a genuine question :) Cheers GAvin chris.ne...@utoronto.ca wrote: Gavin, I wish you the best of luck. Perhaps somebody else on the list can help you. -- original message -- Thanks Chris I have equilibrated the system at 600 K in a previous run therefore would it not be equilibrated, and also would the velocities from the final configuration of the equilibration not be sufficient as equilibrium velocities going into the main simulation Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ener.edr -[no]aver
Also, is anybody aware of what the following option of g_energy performs: -[no]averbool yes Print also the X1,t and sigma1,t, only if only 1 energy is requested If I compare the results of 'g_energy' and 'g_energy -aver', the numbers are the same. Does it mean that g_energy print the averaged values (between nstenergy steps) by default? Vitaly On Fri, Aug 13, 2010 at 6:35 PM, Vitaly Chaban vvcha...@gmail.com wrote: Berk, if I need the average values between 0...N, N...2N, etc - what is the convenient way to get them automatically (in energy.xvg)? Thank you, Vitaly To be more precise, it writes both the current values and the sum over the steps to let g_energy print exact averages. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tpi segmentation fault
Hi all. I am trying to perform a tpi (test particle insertion) calculation on a trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf cluster of Intel(R) Core(TM)2 Quad CPUQ6600 @ 2.40GHz). I am using tpi integrator in the mdp file and the following command: $ grompp -f tpi.mdp -c 32hoa_128dmpcwrun.gro -n index_tpi.ndx -p topol_tpi.top $ mdrun -rerun 32hoa_128dmpcwrun.trr -g tpi.log I tried different versions of gromcas and for 4.0.X I got a segmentation fault getting the message: trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Segmentation fault using a compiled version with config --prefix /home/cerezo/Programs/gromacs4.07 + make + make install. However, it works when I used a precompiled version (got with apt-get, I have kubuntu). So I guess that it may be due to a mistake during the compilation. In addition, other integrators (i.e. md, steep) work correctly with the version I've compiled. My system is and Intel(R) Core(TM)2 Quad CPUQ8400 @ 2.66GHz. Is there any trick I could try in the compilation? I also tried gromacs-4.5-betaX and it works but sometimes (apparently randomly) the calculation gets stops (as if it had entered in an infinite loop) after reading the last frame. Thanks for your attention! Javier -- Javier CEREZO BASTIDA Estudiante de Doctorado - Dpto. Química-Física Universidad de Murcia 30100 MURCIA (España) Tlf.(+34)868887434 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with removing COM translation
On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? cheers, m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with removing COM translation
Em 13-08-2010 14:24, ms escreveu: On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The protein can move without any restriction. To prevent the separation between protein and the water globule, I defined comm_grps = Protein Non-Protein in my .mdp file (I've also used the same groups in temperature coupling as suggested in GMX manual). However, when I run the simulation the protein COM moves away from the center (where it is in the beginning of the simulation) of the water sphere. The movement of COM of the water sphere is small (less than 1 angstron). For simulations of 5ns this translation is about 2 angstrons and for a 14 ns simulation it is more than 10 angstrons. Does anyone could help me with this issue? As far as I know, the remove of COM motion is made by subtracting the COM velocity from the velocity of the atoms within the groups defined in comm_grps. Is it possible to really freeze the movement of the COM of some groups in GROMACS to achieve an absolute static COM? Cheers I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? The idea is to have less water molecules and, consequently, faster simulations. cheers, m. ** Alexandre Suman de Araujo* Faculdade de Ciências Farmacêuticas de Ribeirão Preto* Universidade de São Paulo* Dep. de Física e Química * Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br* Av. do Café, s/n° * e-mail: ale.su...@gmail.com * CEP: 14040-903* Phone: +55 (16) 3602-4172* Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222* ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PCA
I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr files. The eigenvectors were analyzed by g_anaeig program and got eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to know 1. Which file among these shows relative positional fluctuation with eigenvector index. 2. Probability distributions for the displacements along several eigenvectors. 3. Absolute values of the projections of the (normalized) extracted vectors. 4. Cumulative percentage of the motion of a protein from eigvalues.xvg file -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with removing COM translation
On 13/08/10 18:30, Alexandre Suman de Araujo wrote: I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? The idea is to have less water molecules and, consequently, faster simulations. I thought about that, but I guessed you can use a non-cubical box to do (roughly) the same. It seems a nice idea, at a glance. cheers, m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GPU CUDA version does not support improper dihedrals?
Hi, We discussed this a bit off-list, and just figured it would be good to include the conclusions here too so people find it if they search the archives. First, we definitely support all improper torsions of periodic form, such as those in amber, charmm, and opls in OpenMM too, while Gromos uses harmonic torsions. The torsions themselves would actually be straightforward to implement with the customforce classes in OpenMM (slightly slower, but that doesn't matter for torsions). However, this is presently only needed for Gromos force fields, and those won't work with the GPU code anyway since they rely on a full N^2 (where N=natomtypes) matrix for nonbonded parameters that would hurt performance quite a bit on GPUs. This doesn't mean we've ruled out Gromos for future GPU ports (on the contrary, we want to and plan to support it eventually), but it's not priority 1A right now. Cheers, Erik Read and respond to this message at: https://simtk.org/forum/message.php?msg_id=4741 By: Peter Eastman I discussed this with the Gromacs developers to get the full story. It appears that they currently do not support the Gromos force field on GPUs, and it will take a significant amount of work to do so. Improper torsions would actually be easy to handle using a CustomTorsionForce. The real challenge is nonbonded interactions, since Gromos doesn't use consistent combining rules. Hopefully that will happen in a later release. Peter On Aug 10, 2010, at 5:50 PM, chris.ne...@utoronto.ca wrote: This surprised me since most of the systems that I am interested in have improper dihedrals. Is it possible that I did something wrong here? ### Error message from mdrun-gpu: Program mdrun-gpu, VERSION 4.0.99-dev-20100315 Source code file: /project/pomes/cneale/GPC/exe/intel/GPUgromacs/gromacs-4.5-beta2/src/kernel/openmm_wrapper.cpp, line: 610 Fatal error: OpenMM does not support (some) of the provided interaction type(s) (Improper Dih.) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I'm posting again the same topic as http://lists.gromacs.org/pipermail/gmx-users/2010-August/053018.html in case my first post was overlooked in the batch that came through when the mailing list was fixed -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Lindahl lind...@cbr.su.se Professor, Computational Structural Biology Center for Biomembrane Research Swedish e-Science Research Center Department of Biochemistry Biophysics, Stockholm University Tel: +468164675 Cell: +46703844534 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. -Justin Thanks, Juju -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
On Fri, 13 Aug 2010 18:23:40 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. Or, you can just tell g_energy to calculate the density - if it's constant then so is the volume... -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
Jussi Lehtola wrote: On Fri, 13 Aug 2010 18:23:40 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. Or, you can just tell g_energy to calculate the density - if it's constant then so is the volume... Density terms are not printed during NVT, and actually, now that I look into it, neither are the box vectors. If it's NVT, they're fixed. So, in a way, if your .edr file has no box or density information, the NVT was correct. You can also look at the output .gro file - the box vectors should be the same as the ones you started with. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
Thanks Justin, but I did not find them, what I found are Vir-XY, YZ, XX, Are these the same as Box-X, Y, Z, or perhaps can be converted to? Btw, I am using 4.0.7 version. One more Q', I saw your great gromacs tutor...@vt, but I am kinda confused you used both NPT and NVT in position restraint step, while 'official' tutorial by JE Kerrigan only used NPT, would that affect the final results? Sorry, newbie here. Best, Juju From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Fri, August 13, 2010 3:23:40 PM Subject: Re: [gmx-users] Check V for NVT Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. -Justin Thanks, Juju -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
Thanks guys, Sorry, I did not find Density in version 4.0.7. nor Box-X, Y, Z. Any other way out? Best, Juju From: Jussi Lehtola jussi.leht...@helsinki.fi To: gmx-users@gromacs.org Sent: Fri, August 13, 2010 3:29:56 PM Subject: Re: [gmx-users] Check V for NVT On Fri, 13 Aug 2010 18:23:40 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. Or, you can just tell g_energy to calculate the density - if it's constant then so is the volume... -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
When you run an NVT simulation the box coordinates are not written out in the edr file. You can try to extract the box information from your trajectory files. On Fri, Aug 13, 2010 at 6:42 PM, Rama G jujur...@yahoo.com wrote: Thanks guys, Sorry, I did not find Density in version 4.0.7. nor Box-X, Y, Z. Any other way out? Best, Juju -- *From:* Jussi Lehtola jussi.leht...@helsinki.fi *To:* gmx-users@gromacs.org *Sent:* Fri, August 13, 2010 3:29:56 PM *Subject:* Re: [gmx-users] Check V for NVT On Fri, 13 Aug 2010 18:23:40 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. Or, you can just tell g_energy to calculate the density - if it's constant then so is the volume... -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
Rama G wrote: Thanks Justin, but I did not find them, what I found are Vir-XY, YZ, XX, Are these the same as Box-X, Y, Z, or perhaps can be converted to? Btw, I am using 4.0.7 version. See the latest post in the thread. The Vir-* terms refer to virial, which is unrelated. One more Q', I saw your great gromacs tutor...@vt, but I am kinda confused you used both NPT and NVT in position restraint step, while 'official' tutorial by JE Kerrigan only used NPT, would that affect the final results? Sorry, newbie here. Are any of the tutorials official? They're all just contributed by users... In any case, the typical equilibration steps involve both NVT (to relax temperature), then NPT (to relax pressure once temperature is stable). In some cases, if you apply NPT directly, bad clashes in the initial structure can cause temperature spikes, thus kinetic energy spikes, the virial (and thus pressure) goes haywire, and the whole system collapses. Not always the case, but I've noticed that this can happen. Maybe there's a more deeply theoretical reason for NVT prior to NPT, but I've never found one aside from stability issues. Some systems are robust enough to proceed to NPT immediately, but most often in the literature NVT precedes NPT. -Justin Best, Juju *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Fri, August 13, 2010 3:23:40 PM *Subject:* Re: [gmx-users] Check V for NVT Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. -Justin Thanks, Juju -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Check V for NVT
Rama G wrote: Thanks guys, Sorry, I did not find Density in version 4.0.7. nor Box-X, Y, Z. Any other way out? The very absence of these terms indicates that your volume was constant. What purpose do you have for checking it? Do you think something went wrong? If a simple NVT didn't work, the developers would have a pretty serious problem on their hands ;) -Justin Best, Juju *From:* Jussi Lehtola jussi.leht...@helsinki.fi *To:* gmx-users@gromacs.org *Sent:* Fri, August 13, 2010 3:29:56 PM *Subject:* Re: [gmx-users] Check V for NVT On Fri, 13 Aug 2010 18:23:40 -0400 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find Volume in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file. From these, you can calculate the volume. Or, you can just tell g_energy to calculate the density - if it's constant then so is the volume... -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi mailto:jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi mailto:jussi.leht...@helsinki.fi -- -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella histograms
Your language was not rude, but I did get frustrated after twice asking you to perform an analysis and twice being ignored. My advice still stands: plot the deviation vs. time and report back to the list. Chris. -- original message -- Cheers and thanks for the suggestions. P.S. I hope you don't think that the previous msg was in anyway rude. It was actually a genuine question :) Cheers GAvin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] editconf
- Original Message - From: abdullah ahmed abdullah_renk_ah...@hotmail.com Date: Saturday, August 14, 2010 1:05 Subject: [gmx-users] editconf To: gmx gmx-users@gromacs.org --- | Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: - Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) That's not quite the purpose of pdb2gmx. pdb2gmx generates the molecular topology in the .top file, and sanitizes the contents of the coordinate file, *by default* writing a .gro file. You could write this file in another format if you chose. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File - Run editconf to define the box (editconf -d 1) - run gromp and mdrun for the minimization - Run editconf to re-convert back to pdb You can use mdrun -c confout.pdb to do this last step directly. Unfortunately doing this seems to be adding some information into the pdb file that is not related to the atom coordinates. I think this might be trajectory data. Is there someway to remove this info? I can't imagine what you mean. Did you use editconf on the .xtc or .trr file? In future, it's always a good idea to include your actual commands via copy-and-paste, else we are reduced to guessing whether you've done various things right or wrong, and that wastes our time and might not get you the help you need :-) Here, a small sample of the unrelated information might also have helped us understand the issue. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_gyrate -p = Calculate the radii of gyration about the principal axes
Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got = 0.922754 1.22249 1.25603 but in some paper, the authors got = 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the principal axes ? i have checked the Gromacs manual but see nothing there. Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parallel mdrun not working on gentoo linux
Hi All, I am trying to build gromacs-4.0.7 on my gentoo box. My non-parallel version of mdrun is working without any issues but when I try to run the parallel version of mdrun, it kind of hangs (even no help info). Some details- 1) $uname -a Linux bingo 2.6.34-gentoo-r1 #7 SMP Fri Aug 13 10:18:23 IST 2010 i686 Intel(R) Core(TM)2 Quad CPU Q8200 @ 2.33GHz GenuineIntel GNU/Linux 2) openmpi -version : 1.4.1 (through emerge) 3) $ ldd /usr/local/bin/mdrun_mpi linux-gate.so.1 = (0xb77f6000) libmd_mpi.so.5 = /usr/local/gromacs/lib/libmd_mpi.so.5 (0xb76ee000) libgmx_mpi.so.5 = /usr/local/gromacs/lib/libgmx_mpi.so.5 (0xb746) libxml2.so.2 = /usr/lib/libxml2.so.2 (0xb7321000) libz.so.1 = /lib/libz.so.1 (0xb730d000) libnsl.so.1 = /lib/libnsl.so.1 (0xb72f5000) libfftw3f.so.3 = /usr/lib/libfftw3f.so.3 (0xb71b2000) libm.so.6 = /lib/libm.so.6 (0xb718d000) libSM.so.6 = /usr/lib/libSM.so.6 (0xb7184000) libuuid.so.1 = /lib/libuuid.so.1 (0xb717f000) libICE.so.6 = /usr/lib/libICE.so.6 (0xb7166000) libX11.so.6 = /usr/lib/libX11.so.6 (0xb7041000) libxcb.so.1 = /usr/lib/libxcb.so.1 (0xb7025000) libXau.so.6 = /usr/lib/libXau.so.6 (0xb7021000) libXdmcp.so.6 = /usr/lib/libXdmcp.so.6 (0xb701b000) libdl.so.2 = /lib/libdl.so.2 (0xb7017000) libmpi.so.0 = /usr/lib/libmpi.so.0 (0xb6f84000) libopen-rte.so.0 = /usr/lib/libopen-rte.so.0 (0xb6f3d000) libopen-pal.so.0 = /usr/lib/libopen-pal.so.0 (0xb6ed2000) libutil.so.1 = /lib/libutil.so.1 (0xb6ece000) libpthread.so.0 = /lib/libpthread.so.0 (0xb6eb5000) libc.so.6 = /lib/libc.so.6 (0xb6d6f000) /lib/ld-linux.so.2 (0xb77f7000) Please somebody tell me what is the problem? Thanks, Manik Mayur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
