Hi, The .cpt defines the state, not the number of steps to go for.
Setting nsteps to -1 should work for the new (>4.5 definitely, >4.0 I'm not sure) versions of gromacs. I think it was introduced right after the -maxh option was. @Xavier: I added a number of editing options to tpbconv (4.5.1), among which the possibility to set the number of steps directly (which can then be set to -1). You can take the source code from /data_new3/tsjerk/GMX/gromacs-4.5.1-rtc/src/kernel/tpbconv.c Groetjes, Tsjerk On Thu, Feb 24, 2011 at 1:35 PM, XAvier Periole <[email protected]> wrote: > > 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 doesn’t 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 thewww 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
