----- Original Message ----- From: Hsin-Lin Chiang <jian...@phys.sinica.edu.tw> Date: Monday, November 22, 2010 14:51 Subject: Re: [gmx-users] extending simulation without cpt file To: gmx-users@gromacs.org
> Hi, Mark > > So, You mean I can get correct extending simulation without > using -e ede and -t trr in GROMACS ver.4. Yes. That's what the link you gave says. Mark > Then I can set my mind at rest. > > Thank you for your reply. > > Hsin-Lin > >>Hi, Today I use serach and find this topic. > >> > >>I got confused. > >> > >> > >> > >>http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > >> > >>According the page of "extending simulation", in GROMACS > ver.4, the commend is: > >> > >> > >> > >>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr > >So you've created a new .tpr with a longer simulation time (but which > >incidentally has the state of the previous .tpr)... > > > >>mdrun -s next.tpr -cpi previous.cpt > >... and told mdrun to use that longer time, and the current > state in the > >checkpoint file. This will work, so long as you are not > attempting to > >change the thermodynamic ensemble, or similar. > > > >Mark > > > >>I use this two lines to continue my simulation and get success. > >> > >>But now I'm much worried my data is wrong since I didn't use - > e edr and -t trr as in the first line above. > >> > >>The way that tpbconv should -e -t files is written in the part > ver. 3.3.3 and before. > >> > >>My GROMACS version is 4.0.5. > >> > >>Am I right to use lines above to do extending simulation? > >> > >> > >> > >>Hsin-Lin > >> > >> > >> > >>>----- 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 > >> > >> > >> > >> > >> > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: http://lists.gromacs.org/pipermail/gmx- > users/attachments/20101122/437e2152/attachment.html> > >------------------------------ > > > > -- > 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
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