[gmx-users] addition of all hydrogens in pdb2gmx
Hi, The manual says, pdb2gmx adds all hydrogens, including those for carbons. But I could not find the output gro file to contain all the hydrogens (especially for carbons) satisfying all the valencies. Is there any option that I may be missing? thanks, begin:vcard fn:Sridhar Acharya, M n:Malkaram;Sridhar Acharya org:University of Nebraska-Lincoln;Center for Biotechnology adr:Apt # 13;;2325, 'S' St;Lincoln;Nebraska;68503;USA email;internet:[EMAIL PROTECTED] title:Post Doctoral Fellow tel;work:1 402 472 6052 tel;home:1 402 570 8997 tel;cell:1 402 570 8997 x-mozilla-html:TRUE version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PCA multiple outputs from g_anaeig
Hello, g_anaeig analyzes the eigen vectors from eigenvec.trr and eigenval.xvg generated by g_covar and writes the proj.xvg, 2d_proj.xvg, 3d_proj.xvg, filtered.xvg. etc. My question is., For a single run of g_anaeig only a specific 2d_proj.xvg (say between eigenvec 1 and 8), 3d_proj.xvg. etc could be written. But one may want to study the projections between 1 and 2, 1 and 3, 2 and 3. etc. Is there any way to simultaneously write all the desired projections and filtered trajectories from a single run of g_anaeig, since all the required information will be already read once by the program. Any contributors for this? Thanks in advance. sridhar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem reading large file in g_covar
# -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] Phone: Lab: +91-8413-235467*2044 Home: +91-40-27505833 Mobile: +91-9866147193 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem reading large file in g_covar
Hello, I am running g_covar. But the program halts with the error message that the given xtc file was not found. In fact the xtc file which is 7.1GB was very much existing. I suppose that it is a case of large file. I compiled GROMACS3.1.4 with --enable-largefile. But still the same error occurs. How to make g_covar recognise this file? ## :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.1.4 (-: Copyright (c) 1991-2002, University of Groningen, The Netherlands This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar (-: Option Filename Type Description -f50NS_WT.xtc Input Generic trajectory: xtc trr trj gro g96 pdb -s ../FILES/b4md_1cyp_WT.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb -n ../FILES/pr_1cyp_WT.ndx Input, Opt! Index file -o eigenval_WT.xvg Outputxvgr/xmgr file -v eigenvec_WT.trr OutputFull precision trajectory: trr trj -av average_WT.pdb OutputGeneric structure: gro g96 pdb -l covar_WT.log OutputLog file -xpm covar.xpm Output, Opt. X PixMap compatible matrix file -xpmacovara.xpm Output, Opt. X PixMap compatible matrix file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -b time 12000 First frame (ps) to read from trajectory -e time 5 Last frame (ps) to read from trajectory -dt time -1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h -[no]fit boolyes Fit to a reference structure -[no]ref bool no Use the deviation from the conformation in the structure file instead of from the average -[no]mwa bool no Mass-weighted covariance analysis -lastint -1 Last eigenvector to write away (-1 is till the last) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Choose a group for the least squares fit Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 (Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group10 ( Prot-Masses) has 4858 elements Group11 ( Non-Protein) has 36962 elements Group12 (HEME) has47 elements Group13 ( SOL) has 36912 elements Group14 ( CL-) has 3 elements Group15 ( Other) has 36962 elements Group16 (Protein_HEME) has 4905 elements Group17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Choose a group for the covariance analysis Group 0 ( System) has 41820 elements Group 1 ( Protein) has 4858 elements Group 2 ( Protein-H) has 3775 elements Group 3 ( C-alpha) has 478 elements Group 4 (Backbone) has 1434 elements Group 5 ( MainChain) has 1913 elements Group 6 (MainChain+Cb) has 2361 elements Group 7 ( MainChain+H) has 2363 elements Group 8 ( SideChain) has 2495 elements Group 9 ( SideChain-H) has 1862 elements Group10 ( Prot-Masses) has 4858 elements Group11 ( Non-Protein) has 36962 elements Group12 (HEME) has47 elements Group13 ( SOL) has 36912 elements Group14 ( CL-) has 3 elements Group15 ( Other) has 36962 elements Group16 (Protein_HEME) has 4905 elements Group17 (Protein_HEME_CL-) has 4908 elements Select a group: 3 Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. Constructing covariance matrix (1434x1434)... Fatal error: File 50NS_WT.xtc not found # -- Sridhar Acharya, M Senior Research Fellow Lab
Re: [gmx-users] MD continuation runs in serial but not in parallel
I did not use -shuffle -t to run this. However even when I use -shuffle option the same error occurs. From: Sridhar Acharya [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] MD continuation runs in serial but not in parallel Date: Mon, 03 Jul 2006 17:56:27 +0530 Dear GMX users, I used grompp with -t option to continue a serially run simulation to run in parallel. I have given gen_vel = no in the .mdp file. But mdrun with -np 2 stops and reports the following error. (md.log file is given below) The same simulation could be continued in serial without any error. What is the cause for this descrepancy? Any parameters to be set? # Going to use C-settle (5335 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.42 4862 4887 0.07 After LINCS 0.49 4880 4881 0.10 Started mdrun on node 0 Mon Jul 3 18:48:47 2006 Initial temperature: 301.39 K Grid: 17 x 14 x 19 cells Step Time Lambda Annealing 00.00.01.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.058480 3573 3574 0.005918 After LINCS 0.000140 3842 3844 0.20 t = 0.000 ps: Water molecule starting at atom 17176 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.10484e+033.58568e+032.61866e+031.41412e+034.86285e+04 LJ (SR) Coulomb (SR) Coulomb (LR) PotentialKinetic En. 2.14166e+08 -5.54411e+05 -1.31762e+052.13544e+08nan Total EnergyTemperature Pressure (bar) nannannan ## -- Did you use the -shuffle option of grompp? With grompp -shuffle -t grompp expectes a shuffled trajectory. Berk. -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Continuation of Serial MD simulation in Parallel
p for User2 containing 41820 elements Making dummy/rest group for XTC containing 41820 elements Making dummy/rest group for Or. Res. Fit containing 41820 elements T-Coupling has 4 element(s): Protein HEME SOL CL- Energy Mon. has 4 element(s): Protein HEME SOL CL- Acceleration has 1 element(s): rest Freeze has 1 element(s): rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest Checking consistency between energy and charge groups... getting data from old trajectory ... Reading Coordinates and Box size from old trajectory Will read till time 2 Velocities generated: ignoring velocities in input trajectory trn version: GMX_trn_file Reading frame 680 time 19997.312 Using frame at t = 2 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117 splitting topology... Walking down the molecule graph to make shake-blocks There are 14390 charge group borders and 12308 shake borders There are 12308 total borders Division over nodes in atoms: 10455 10455 10455 10455 writing run input file... Back Off! I just backed up test.tpr to ./#test.tpr.4# There were 7 warnings gcq#142: "It Was My Pleasure" (Pulp Fiction) ##### -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Continuation of Serial MD simulation in Parallel
Thanks so much for the answer. I have one more doubt. Could you please answer? I could make the change and run, but still the following line in the log file, "Starting time for run is 0 ps" (BLUE color), appears controversial to me. The log message is as follows. ## Checking consistency between energy and charge groups... getting data from old trajectory ... Reading Coordinates, Velocities and Box size from old trajectory Will read till time 2 trn version: GMX_trn_file Reading frame 60 time 19917.312 Using frame at t = 2 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117 splitting topology... Walking down the molecule graph to make shake-blocks There are 14390 charge group borders and 12308 shake borders There are 12308 total borders Division over nodes in atoms: 10455 10455 10455 10455 writing run input file... ### Dallas B. Warren wrote: So I am generating .tpr file as follows using the command as follows. Does the log message (Highlighted in RED) "Velocities generated: ignoring velocities in input trajectory", means that the simulation wont be continuation of the earlier one? That warning tells you that in your .mdp file you have velocity generation on, turn that option off. You don't want that if you want a continuation of the run. The velocity of the atoms is taken from the .trr file that you feed to grompp. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD continuation runs in serial but not in parallel
Dear GMX users, I used grompp with -t option to continue a serially run simulation to run in parallel. I have given gen_vel = no in the .mdp file. But mdrun with -np 2 stops and reports the following error. (md.log file is given below) The same simulation could be continued in serial without any error. What is the cause for this descrepancy? Any parameters to be set? # Going to use C-settle (5335 waters) wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1 Constraining the coordinates at t0-dt (step -1) Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.42 4862 4887 0.07 After LINCS 0.49 4880 4881 0.10 Started mdrun on node 0 Mon Jul 3 18:48:47 2006 Initial temperature: 301.39 K Grid: 17 x 14 x 19 cells Step Time Lambda Annealing 00.00.01.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.058480 3573 3574 0.005918 After LINCS 0.000140 3842 3844 0.20 t = 0.000 ps: Water molecule starting at atom 17176 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 8.10484e+033.58568e+032.61866e+031.41412e+034.86285e+04 LJ (SR) Coulomb (SR) Coulomb (LR) PotentialKinetic En. 2.14166e+08 -5.54411e+05 -1.31762e+052.13544e+08nan Total EnergyTemperature Pressure (bar) nannannan ## -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can a Serial MD simulation be continued in Parallel?
Dear GMX-users I want to know whether a MD simulation that was run as a serial job could be continued in parallel using tpbconv? If so, how to give the number of processors for the command? Regards, sridhar -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Can a Serial MD simulation be continued in, Parallel?
Hi, But will that not do a new simulation rather than an exact continuation of the previous simulation? sridhar -- Message: 4 Date: Thu, 29 Jun 2006 18:48:45 +1000 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Can a Serial MD simulation be continued in Parallel? To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Sridhar Acharya wrote: Dear GMX-users I want to know whether a MD simulation that was run as a serial job could be continued in parallel using tpbconv? If so, how to give the number of processors for the command? There's no reason you couldn't use grompp with the .trr and .edr files as inputs to generate a .tpr for a different number of processors. There must be a numerical perturbation to your model physics in doing so - you're adding up lists of numbers in different orders - but the effect should be negligible within the MM approximation. Mark -- begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Need topology for selenomethionine
Hi all, Has anybody built a gromax topology for selenomethionine? How the topology can be incorporated into the existing gromacs topology files? thanks in advance. sridhar -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with selenomethionine residues
Hi, When I am running the mdrun for position restrain the program terminates giving the following error. The protein molecule contains 16 selenomethionine residues, the topology for which was got from the PRODRG server. When run in GROMACS 3.2.1 version === Wrote pdb files with previous and current coordinates Fatal error: ci = -2147483648 should be in 0 .. 6782 [FILE nsgrid.c, LINE 218] When run in GROMACS 3.3.1 version === Fatal error: Too many LINCS warnings (12461) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations. If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. Looking forward for ur response, regards sridhar -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with continuation of simulation
Hello, I had carried out a 20ns protein simulation on Gromacs v3.2.1. Later I continued the simulation on Gromacs v3.3. I ran the following command supplying the energy file and trajectory file. But the program gave error and stopped (log message is given below). Since I read that supply of energy file is not absolutely required. I again ran tpbconv without -e option for another 10ns. This time the program ran with the warning message that the continuation will not be exact. WARNING: The simulation uses pressure and/or Nose-Hoover temperature coupling, the continuation will only be exact when an energy file is supplied. When I plotted the trajectory of the Potential energy, I found the difference, with PE much below than the previous simulation (PE dropped from -559000 to -561000). Can I use the data of this additional simulation, or is it a drastic variation, that I need to take care of? Thank you, expecting your suggessions. ## [EMAIL PROTECTED] TRAJEC_WT]$ tpbconv -s ../OTHERS_WT/b4md_1cyp_WT.tpr -f rerereafter15_WT.trr -e ../OTHERS_WT/rerereafter15_WT.edr -o new.tpr -until 3 :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2004, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) tpbconv (-: Option Filename Type Description -s ../OTHERS_WT/b4md_1cyp_WT.tpr InputGeneric run input: tpr tpb tpa xml -f rerereafter15_WT.trr Input, Opt! Full precision trajectory: trr trj -e ../OTHERS_WT/rerereafter15_WT.edr Input, Opt! Generic energy: edr ene -n index.ndx Input, Opt. Index file -onew.tpr Output Generic run input: tpr tpb tpa xml Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 0 Set the nicelevel -time real -1 Continue from frame at this time (ps) instead of the last frame -extend real 0 Extend runtime by this amount (ps) -until real 3 Extend runtime until this ending time (ps) -[no]zeroq bool no Set the charges of a group (from the index) to zero -[no]unconstrained boolyes For a continuous trajectory, the constraints should not be solved before the first step (default) Reading toplogy and shit from ../OTHERS_WT/b4md_1cyp_WT.tpr Reading file ../OTHERS_WT/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision) Note: tpx file_version 24, software version 40 Note: nLincsIter not in run input file, setting it to 1 Modifying ir-bUncStart to TRUE READING COORDS, VELS AND BOX FROM TRAJECTORY rerereafter15_WT.trr... trn version: GMX_trn_file (single precision) Read frame684: step 341344 time 2.000 Using frame of step 341344 time 2 Opened ../OTHERS_WT/rerereafter15_WT.edr as single precision energy file Reading frame 60 time 19917.312 --- Program tpbconv, VERSION 3.3 Source code file: enxio.c, line: 358 Fatal error: Could not find energy term named 'Pcoupl-Mu-XX' --- Stop Drinking My Beer ! (The Amps) # -- Sridhar Acharya, M Senior Research Fellow Lab of Computational Biology CDFD, Gandipet Campus Hyderabad. AP. INDIA http://www.cdfd.org.in email: [EMAIL PROTECTED] Phone: Lab: 08413-235467*2044 Mobile: 9866147193 begin:vcard fn:Sridhar Acharya n:Acharya;Sridhar org:CDFD;Computational Biology adr:;;Gandipet Campus;Hyderabad;AP;;INDIA email;internet:[EMAIL PROTECTED] title:Senior Research Fellow tel;work:08413-235467*2044 tel;home:040-27505833 tel;cell:9866147193 x-mozilla-html:TRUE url:http://www.cdfd.org.in version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use
