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Hi,<br><br>I fixed the bug for 4.5.4.<br><br>If you want an unlimited number of steps, use:<br>tpbconv -nsteps -1<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] Re: tpbconv extension<br>Date: Mon, 13 Dec 2010 17:44:53 +0100<br><br>
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Hi,<br><br>No this is actually a bug in tpbconv.<br>-nsteps will not work, because that uses a normal int, not a 64-bit integer.<br>-dt should work, but on line 531 of src/kernel/tpbconv.c (int) should be<br>replaced by (gmx_large_int_t).<br><br>But are you sure you want to add a millisecond to your simulation time?<br><br>Berk<br><br><br>> Date: Mon, 13 Dec 2010 11:40:50 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: tpbconv extension<br>> <br>> <br>> <br>> ram bio wrote:<br>> > Hi Justin,<br>> > <br>> > The command was:<br>> > <br>> > tpbconv -s memb12extnr42000ns.tpr -extend 1000000 -o 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 problem. I <br>> believe all of this has been resolved as of Gromacs 4.5, for 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>> >>> 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>> >>>> 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 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 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>
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