Thanks Justin! it works now. Greg
On Wed, Nov 3, 2010 at 7:39 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > ----- Original Message ----- > From: Mark Abraham <mark.abra...@anu.edu.au> > Date: Thursday, November 4, 2010 10:38 > Subject: Re: [gmx-users] extending simulation without cpt file > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > > > > > ----- Original Message ----- > > From: Yongchul Chung <yxc...@case.edu> > > Date: Thursday, November 4, 2010 10:28 > > Subject: [gmx-users] extending simulation without cpt file > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > > > Hello gmxers, > > > > > > I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file > but erased cpt file. However, I need to extend the simulation from the end > of the trajectory file. I know this will not be binary identical as stated > here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). > I used following commands. > > > > > > tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr > > > mdrun -s topolnew.tpr > > > > > > When I do this and run the simulation, for some reason, the simulation > starts from t=0 instead of t=102000. it seems like gromacs is writing the > file without recognizing it that it should start the trajectory from 102000 > ps. Is this a known bug? If so, is there a way around to solve this problem? > > > > You've extended the run time of the original simulation, and forced it > to start from the state in the new .tpr, but that state came from the > original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that > of the checkpoint. > > > > Your best chance of continuing will come from reconstructing the .mdp > suitably (use gmxcheck to compare resulting .tpr files) and using grompp to > create a .tpr using the most recent endpoint permitted by your .trr + .edr. > > Actually, Justin's right. tpbconv needs -e -t files. It's been so long > since I used it, I'd forgotten :-) > > Mark > > -- > 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 >
-- 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