Using the cpt file didn't work for me - it remembered the nsteps and quit before even running anything. Without getting into the details, I am changing the temperature along the way in my simulation and therefore I can't use nsteps -1 either. But Xavier's first suggestion worked, so I will continue using that solution...
Thanks, Jesper -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of XAvier Periole Sent: 24. februar 2011 13:35 To: Discussion list for GROMACS users Subject: Re: [gmx-users] negative steps from tpbconv I am not sure the use of cpt would work! I might have tried and got a problem since the cpt might define where it is going (nsteps) ... to be tried! @Tsjerk: I have not been able to use the nsteps set to -1 for some reason it was telling it had ran enough! Any idea why would that be? On Feb 24, 2011, at 1:01 PM, Tsjerk Wassenaar wrote: > Hi Jesper, > > Using a .cpt file will also work with the modified .tpr file. > Maybe it is also worth considering using the -maxh option to mdrun, > with nsteps in the .mdp file set to -1 (run infinitely). That avoids > the hassle with extensions. > > Cheers, > > Tsjerk > > 2011/2/24 Jesper Sørensen <[email protected]>: >> Hi Xavier, >> >> >> >> That worked, thanks Would it also work if I just gave the old >> state.cpt file to mdrun? >> >> >> >> Jesper >> >> >> >> From: [email protected] >> [mailto:[email protected] >> ] >> On Behalf Of XAvier Periole >> Sent: 24. februar 2011 12:19 >> To: Discussion list for GROMACS users >> Subject: Re: [gmx-users] negative steps from tpbconv >> >> >> >> >> >> Hi Jesper, >> >> >> >> This occurs when you ask for a number of steps that exceed the >> >> the size of an integer! I got the same problem recently ... >> >> >> >> The only solution I found was to make a new mdp file where t0 >> >> is the old time and asking for the extension you need ... you can >> >> give trr and edr files to grompp so the tpr file is a continuation of >> >> earlier one ... >> >> >> >> XAvier. >> >> >> >> On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote: >> >> Hi, >> >> >> >> I am trying to extend the run time in tpr file to include more steps >> using tpbconv >> >> This has worked well for a while, but now I get two errors >> >> One is that it writes now -2074660000 steps, which doesnt make >> sense why is this number negative >> >> Also, You've simulated long enough. Not writing tpr file >> >> >> >> If I extend the simulation using the nsteps flag, then it will write >> the tpr file, but still comes up with negative numbers whens starting >> mdrun with the file, which mdrun does not exactly like. >> >> >> >> Output is a s follows: >> >> READING COORDS, VELS AND BOX FROM TRAJECTORY >> ../T305/512DPPC_9728W_305K_625ns.trr... >> >> >> >> trn version: GMX_trn_file (single precision) >> >> Read trr frame 4166: step 2124660000 time 53116500.000 >> >> >> >> Using frame of step 2124660000 time 5.31165e+07 >> >> Extending remaining runtime of by 625000 ps (now -2074660000 steps) >> >> You've simulated long enough. Not writing tpr file >> >> >> >> Best regards, >> >> Jesper >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials University of Groningen The > Netherlands > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
