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
