can extend simulation if the number of steps were reached. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
That said, does extending the simulation avoid the problems that you found in the simulation? On Tue, Sep 1, 2015 at 11:54 PM, Johnny Lu <[email protected]> wrote: > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts > > > > On Tue, Sep 1, 2015 at 11:53 PM, Johnny Lu <[email protected]> wrote: > >> the position in xtc is not accurate enough for restarting simulation. xtc >> has no velocity. >> >> restart need position, velocity, and variables for the thermostat and >> barostat. >> >> Do you have any cpt file? may be you can run a restart using cpt and tpr >> files. >> >> On Mon, Aug 31, 2015 at 10:21 PM, Adriana Garro <[email protected] >> > wrote: >> >>> :-( ok >>> Thanks, I will have to run this simulation again. >>> Bye >>> >>> Adriana >>> >>> *********************************************************** >>> Dra. Adriana D. Garro >>> Química Medicinal >>> Facultad de Química, Bioquímica y Farmacia >>> Universidad Nacional de San Luis >>> IMASL-CONICET >>> San Luis, Argentina >>> >>> Tel..............:+54 266 4424689 int 6153 >>> e-mail...: [email protected] >>> e-mail...: [email protected] >>> >>> >>> ********************************************************** >>> >>> 2015-08-31 23:17 GMT-03:00 Justin Lemkul <[email protected]>: >>> >>> > >>> > >>> > On 8/31/15 11:52 AM, Adriana Garro wrote: >>> > >>> >> Dear Gromacs users, >>> >> >>> >> My 100 ns simulation finish but in a wrong way, I knew it when I >>> tried to >>> >> use an analizing tool and the message was the next one >>> >> >>> >> Fatal error: >>> >> Magic Number Error in XTC file (read 0, should be 1995) >>> >> >>> >> It seems that this kind of error is related to the network file >>> system. >>> >> My first attempt was restart (I am using gromacs 4.5.5) >>> >> mdrun -s topol.tpr -cpi state.cpt >>> >> but of course it finished immediately then I realized that the number >>> of >>> >> steps was reached. >>> >> >>> >> I did a copy of the md.xtc file while it was running in order to see >>> how >>> >> things were going on, aproximately at 85 ns, so I would like to know >>> if it >>> >> is possible to extend my simulation using this 85ns xtc file. (without >>> >> having cpt file) >>> >> >>> >> >>> > The .xtc has nothing useful about the state of the simulation. A set >>> of >>> > coordinates is inadequate for properly continuing a simulation. >>> > >>> > -Justin >>> > >>> > -- >>> > ================================================== >>> > >>> > Justin A. Lemkul, Ph.D. >>> > Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> > >>> > Department of Pharmaceutical Sciences >>> > School of Pharmacy >>> > Health Sciences Facility II, Room 629 >>> > University of Maryland, Baltimore >>> > 20 Penn St. >>> > Baltimore, MD 21201 >>> > >>> > [email protected] | (410) 706-7441 >>> > http://mackerell.umaryland.edu/~jalemkul >>> > >>> > ================================================== >>> > -- >>> > Gromacs Users mailing list >>> > >>> > * Please search the archive at >>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> > posting! >>> > >>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> > >>> > * For (un)subscribe requests visit >>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> > send a mail to [email protected]. >>> > >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to [email protected]. >>> >> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
