I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns.
I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan <rajatdesi...@gmail.com>wrote: > 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 > -- 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
