Dear Tsjerk, Thank for your help. tbpconv -time works fine. Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Physics and Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
________________________________ From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar Sent: Sun 3/18/2007 6:31 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Restarting a gromacs calcluation Hi Luciano, It may be a good idea to think about the contents of the different files and the meaning of the messages. If you don't provide a .trr file, you won't have new coordinates, tpbconv will use those from the original .tpr and effectively, you will just start the run all over! Man..., what about tpbconv -h, and following tpbconv with -time to select a frame for which you have positions, velocities and energies? Tsjerk On 3/17/07, Triguero, Luciano O <[EMAIL PROTECTED]> wrote: > >> Dear Users, > >> > >> Thank for your help. I started a 10 ns simulation, but it dies because of > >> an error in the cluster PBS system, so I want to continue the simulation > >> from the last (r,v) point. May I still use tpbconv to restart from that > >> last point and continue the simulation. > >> > Check where your trr or edr file ends using gmxcheck -f or -e. The > shorter will be used by tpbconv for your new tpr. Specify tpbconv with > -f and -e. > > Dear, > > Thank for your answer. I still have a problem. Do you mean (-f and -e) or (-f > or -e) > > I checked my trr and edr files and edr files ends first, then I typed: > > tpbconv -s md_input.tpr -f <>.trr -e <>.edr -o md_cont.tpr > > and got the following error message: > > ++++++++++++++++++++++++++++++++++++++++++++++++++ > Opened md_minim_energy.edr as single precision energy file > Reading frame 4000 time 4000.000 > Last frame read 4876 > WARNING: Incomplete frame: nr 4877 time 4876.000 > ------------------------------------------------------- > Program tpbconv, VERSION 3.3.1 > Source code file: enxio.c, line: 401 > Fatal error: > Could not find frame with time 4884.000000 in 'md_minim_energy.edr' > +++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > However, tpbconv runs without error when I provide only option -e <>.edr. Is > it correct to restart > a calculation with the .tpr file generated with only -e <>.edr option. Will > be then possible to concatenate trajectories correctely? > > Advices, > > Thank for your time, > > Luciano > > > > > > > Sure - as far as I know. It will generate new .tpr, which you will use for > > starting the simulation - when it is finished, simply concatenate > > trajectories, energy files with trjcat and eneconv. > > > > Milan > > > > > >> Thank again, > >> > >> Luciano > >> > >> Dr. Luciano Triguero College of Art and Science Department of Physics and > >> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 > >> Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 > >> > >> ________________________________ > >> > >> From: [EMAIL PROTECTED] on behalf of Yang Ye > >> Sent: Fri 3/16/2007 8:49 AM > >> To: Discussion list for GROMACS users > >> Subject: Re: [gmx-users] Restarting a gromacs calcluation > >> > >> > >> > >> Can you be more specific? Continue or start new simulation. Use tpbconv > >> to extend your simulation. > >> > >> On 3/16/2007 9:37 AM, Triguero, Luciano O wrote: > >> > >>> Dear users, > >>> > >>> How do I restart a gromacs simulation? > >>> > >>> Ciao, > >>> > >>> Luciano > >>> > >>> Dr. Luciano Triguero College of Art and Science Department of Physics and > >>> Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box > >>> 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: > >>> 305-284-3938 _______________________________________________ > >>> gmx-users mailing list gmx-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 mailing list gmx-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 mailing list gmx-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 mailing list gmx-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 mailing list gmx-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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-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
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