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Sorry, I mistook a million ps for a millisecond, this is a microsecond.<br>The maximum number of steps in version 4.0 is INT_MAX, which is 2,147,483,647.<br>From the name of your tpr file it seems you are not exceeding this,<br>so I don't know what's wrong exactly.<br><br>But for this reason (and many other reasons), you might want to consider<br>upgrading to 4.5.3 (and possibly applying the bug-fix I mailed before).<br><br>Berk<br><br>> Date: Mon, 13 Dec 2010 17:56:43 +0100<br>> Subject: Re: [gmx-users] Re: tpbconv extension<br>> From: rmbio861@gmail.com<br>> To: jalemkul@vt.edu; gmx-users@gromacs.org<br>> CC: <br>> <br>> Hi Justin and Berk,<br>> <br>> Thanks for the suggestions.<br>> <br>> I am using gromacs 4.0.7 single precision, and would like to extend my<br>> run each time by 1 microsec as it fits into the wall time on the<br>> server for my system.<br>> Please suggest.<br>> <br>> Thanks<br>> Ram<br>> On Mon, Dec 13, 2010 at 5:40 PM, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> ><br>> ><br>> > ram bio wrote:<br>> >><br>> >> Hi Justin,<br>> >><br>> >> The command was:<br>> >><br>> >> tpbconv -s memb12extnr42000ns.tpr -extend 1000000 -o<br>> >> memb12extnr43000ns.tpr<br>> >><br>> ><br>> > Try using -nsteps instead. There are issues with -extend and -until (bad<br>> > rounding, limits to the size of the number, etc) that can cause this<br>> > problem. I believe all of this has been resolved as of Gromacs 4.5, for<br>> > future reference.<br>> ><br>> > -Justin<br>> ><br>> >> Thanks<br>> >><br>> >> Ram<br>> >><br>> >> On Mon, Dec 13, 2010 at 5:35 PM, Justin A. Lemkul <jalemkul@vt.edu> wrote:<br>> >>><br>> >>> ram bio wrote:<br>> >>>><br>> >>>> Dear Gromacs users,<br>> >>>><br>> >>>> I am running a CG simulation for a peptide in lipid bilayer, and the<br>> >>>> run didnot extend after 42000 ps using gromacs 4.0.7,<br>> >>>><br>> >>>> Reading toplogy and shit from memb12extnr42000ns.tpr<br>> >>>> Extending remaining runtime of by 1e+06 ps (now -2144967266 steps)<br>> >>>> You've simulated long enough. Not writing tpr file<br>> >>>><br>> >>>> Please give your suggestions to overcome this error.<br>> >>>><br>> >>> What was your command?<br>> >>><br>> >>> -Justin<br>> >>><br>> >>>> Ram<br>> >>>><br>> >>>><br>> >>>><br>> >>>><br>> >>>> On Mon, Dec 13, 2010 at 5:26 PM, ram bio <rmbio861@gmail.com> wrote:<br>> >>>>><br>> >>>>> Dear Gromacs users,<br>> >>>>><br>> >>>>> I<br>> >>>>><br>> >>> --<br>> >>> ========================================<br>> >>><br>> >>> Justin A. Lemkul<br>> >>> Ph.D. Candidate<br>> >>> ICTAS Doctoral Scholar<br>> >>> MILES-IGERT Trainee<br>> >>> Department of Biochemistry<br>> >>> Virginia Tech<br>> >>> Blacksburg, VA<br>> >>> jalemkul[at]vt.edu | (540) 231-9080<br>> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> >>><br>> >>> ========================================<br>> >>> --<br>> >>> gmx-users mailing list gmx-users@gromacs.org<br>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> >>> Please search the archive at<br>> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> >>> Please don't post (un)subscribe requests to the list. Use the www<br>> >>> interface<br>> >>> or send it to gmx-users-request@gromacs.org.<br>> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> >>><br>> >><br>> ><br>> > --<br>> > ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]vt.edu | (540) 231-9080<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> ><br>> > ========================================<br>> > --<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at<br>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www interface<br>> > or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>> ><br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br> </body>
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