Thank you!
On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/15/13 8:56 AM, rajat desikan wrote: > >> 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. >> >> > It does not. Checkpoints are recycled every -cpt minutes. You can keep > all checkpoints by using the mdrun -cpnum option, but I suspect that will > use up a lot of disk space. > > > 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. >> >> > Or just re-run the simulation from the same .tpr file you used before. > > -Justin > > >> 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 <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> >>>> <htt**p://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<h**ttp://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> >>>> <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 >>> >>> >> >> >> > -- > ==============================**==================== > > 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
