Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step.
On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/13 8:38 AM, Rajat Desikan wrote: > >> Hi, >> I have a 20 ns long trajectory which has become corrupted beyond 18ns. I >> have the full checkpoint file. Is there any way I can use mdrun and the >> .cpt >> to rerun the simulation from 18ns and append it to the current .xtc >> (After I >> have clipped the part beyond 18ns by trjconv)? I did not find the >> appropriate flag in the mdrun online manual pages. >> > > It's no different than doing any restart. > > mdrun -s topol.tpr -cpi good_state.cpt -noappend > > Then concatenate trajectory and energy files with trjcat and eneconv. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists