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 <li...@jsx.dk>: > Hi Xavier, > > > > That worked, thanks… Would it also work if I just gave the old state.cpt > file to mdrun? > > > > Jesper > > > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > 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 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 > -- 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 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
