No, the point is that in Gromacs version 4.0 (and all versions before) steps were counted in plain int's, which are 32 bit. In version 4.5 they are 64 bit.
But I would suggest to upgrade to 4.5.3 for performance reasons. If you can run a microsecond, you are probably running in parallel over many core and 4.5.3 will also improve your performance. Berk > Date: Mon, 13 Dec 2010 18:16:28 +0100 > Subject: Re: [gmx-users] Re: tpbconv extension > From: rmbio...@gmail.com > To: gmx-users@gromacs.org > > Hi Berk, > > Thanks for the suggestion, does the tpr file generated by the options > mention on PC would work on a server with older version of Gromacs > i.e. 4.0... > > Ram > > On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess <g...@hotmail.com> wrote: > > Sorry, I mistook a million ps for a millisecond, this is a microsecond. > > The maximum number of steps in version 4.0 is INT_MAX, which is > > 2,147,483,647. > > From the name of your tpr file it seems you are not exceeding this, > > so I don't know what's wrong exactly. > > > > But for this reason (and many other reasons), you might want to consider > > upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before). > > > > Berk > > > >> Date: Mon, 13 Dec 2010 17:56:43 +0100 > >> Subject: Re: [gmx-users] Re: tpbconv extension > >> From: rmbio...@gmail.com > >> To: jalem...@vt.edu; gmx-users@gromacs.org > >> CC: > >> > >> Hi Justin and Berk, > >> > >> Thanks for the suggestions. > >> > >> I am using gromacs 4.0.7 single precision, and would like to extend my > >> run each time by 1 microsec as it fits into the wall time on the > >> server for my system. > >> Please suggest. > >> > >> Thanks > >> Ram > >> On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> > > >> > > >> > 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 > > > > -- > > 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
-- 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
