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-us...@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-us...@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-us...@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
