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No, the point is that in Gromacs version 4.0 (and all versions before) steps<br>were counted in plain int's, which are 32 bit. In version 4.5 they are 64 bit.<br><br>But I would suggest to upgrade to 4.5.3 for performance reasons.<br>If you can run a microsecond, you are probably running in parallel<br>over many core and 4.5.3 will also improve your performance.<br><br>Berk<br><br>> Date: Mon, 13 Dec 2010 18:16:28 +0100<br>> Subject: Re: [gmx-users] Re: tpbconv extension<br>> From: rmbio861@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> Hi Berk,<br>> <br>> Thanks for the suggestion, does the tpr file generated by the options<br>> mention on PC would work on a server with older version of Gromacs<br>> i.e. 4.0...<br>> <br>> Ram<br>> <br>> On Mon, Dec 13, 2010 at 6:04 PM, Berk Hess <gmx3@hotmail.com> wrote:<br>> > 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<br>> > 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<br>> >> > (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><br>> >> >> 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<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>> >> 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<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>> ><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<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>> ><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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