Hi No, I don't have a cpt file, I mean I have one but it is the final cpt because the simulation finished (in a wrong way). The problem came up in the last 15 ns, I had checked before and it was going fine. I already reran the simulation but this time using subtrajectories. Thanks!
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...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ********************************************************** 2015-09-02 0:53 GMT-03:00 Johnny Lu <johnny.lu...@gmail.com>: > 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 <adrianagarr...@gmail.com> > 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...: adga...@unsl.edu.ar > > e-mail...: adrianagarr...@gmail.com > > > > > > ********************************************************** > > > > 2015-08-31 23:17 GMT-03:00 Justin Lemkul <jalem...@vt.edu>: > > > > > > > > > > > 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 > > > > > > jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. > > > > > -- > > 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 gmx-users-requ...@gromacs.org. > > > -- > 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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.