Hi, I fixed the bug for 4.5.4.
If you want an unlimited number of steps, use: tpbconv -nsteps -1 Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Re: tpbconv extension Date: Mon, 13 Dec 2010 17:44:53 +0100 Hi, No this is actually a bug in tpbconv. -nsteps will not work, because that uses a normal int, not a 64-bit integer. -dt should work, but on line 531 of src/kernel/tpbconv.c (int) should be replaced by (gmx_large_int_t). But are you sure you want to add a millisecond to your simulation time? Berk > Date: Mon, 13 Dec 2010 11:40:50 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: tpbconv extension > > > > ram bio wrote: > > Hi Justin, > > > > The command was: > > > > tpbconv -s memb12extnr42000ns.tpr -extend 1000000 -o memb12extnr43000ns.tpr > > > > Try using -nsteps instead. There are issues with -extend and -until (bad > rounding, limits to the size of the number, etc) that can cause this problem. > I > believe all of this has been resolved as of Gromacs 4.5, for future reference. > > -Justin > > > Thanks > > > > Ram > > > > On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> > >> ram bio wrote: > >>> Dear Gromacs users, > >>> > >>> I am running a CG simulation for a peptide in lipid bilayer, and the > >>> run didnot extend after 42000 ps using gromacs 4.0.7, > >>> > >>> Reading toplogy and shit from memb12extnr42000ns.tpr > >>> Extending remaining runtime of by 1e+06 ps (now -2144967266 steps) > >>> You've simulated long enough. Not writing tpr file > >>> > >>> Please give your suggestions to overcome this error. > >>> > >> What was your command? > >> > >> -Justin > >> > >>> Ram > >>> > >>> > >>> > >>> > >>> On Mon, Dec 13, 2010 at 5:26 PM, ram bio <rmbio...@gmail.com> wrote: > >>>> Dear Gromacs users, > >>>> > >>>> I > >>>> > >> -- > >> ======================================== > >> > >> Justin A. Lemkul > >> Ph.D. Candidate > >> ICTAS Doctoral Scholar > >> MILES-IGERT Trainee > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> ======================================== > >> -- > >> 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 > >> > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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
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