Re: [gmx-users] Problem with continuation of simulation
Sridhar Acharya wrote: 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. It is not a good idea to change gromacs versions within a project. Obviously in trying to improve the software we fix the bugs that are found, and some of these may influence the results. You probably should finish your project in 3.2.1 and start using 3.3.1 for your next project. Check the website for the differences between the versions of the code. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ 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] Problem with continuation of simulation
Hi, On Tuesday 06 June 2006 11:10, Sridhar Acharya wrote: > 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). Is your tpbconv from version 3.2.1 or 3.31? I would sugguest you take this from version 3.2 and mdrun from 3.3 > > 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) > ### >## Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___
[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
