Thank you Justin for your reply. Pt 3 should be the correct way to proceed. But somehow if I have lost my state.cpt file, can I continue my run using following commands:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene -noappend trjcat -f previous.trr next.trr -o combine.trr On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/21/13 3:46 PM, Nidhi Katyal wrote: > >> Dear all >> I would like to know the difference between restarting our crashed runs by >> 1) first generating next.tpr using tpbconv -extend option >> then running grompp with this *.tpr file >> > > Why would you run grompp? If you're using it as a source of coordinates, > you're going to be dealing with the initial state, not the last state of > the previous simulation, so that's garbage. If you're restarting a crash, > then presumably there is no need at all to invoke tpbconv or grompp. > > > and finally running mdrun but with no cpi option >> > > Makes no sense. You're basically obliterating the previous simulation. > > > 2) same as 1 but with -cpi option >> > > Still no need for grompp, but if providing -cpi to mdrun, you're resuming > from the correct state. > > > 3) using only mdrun command with cpi option and with previous *.tpr >> (ie not creating new tpr by tpbconv option) >> > > This is the correct way to proceed. The run will pick up from the state > stored in the .cpt file and proceed with the number of steps originally > specified in the .tpr file. > > > 4) using procedure 3 but with no state.cpt file >> >> > The run should start over. > > > Secondly, if state.cpt contains all the information to continue the >> simulation then why the simulation should continue at all without >> providing >> these files as in procedure 1 and 4 >> >> > Without a .cpt file, the run starts over from the beginning. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > 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> > -- 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
