mdrun -v -deffnm md -cpi md IIRC the -cpi file is immune from -deffnm
Mark On Tue, Sep 17, 2013 at 4:48 AM, Mahboobeh Eslami <mahboobeh.esl...@yahoo.com> wrote: > dear mark > > yes i do > my comment for md run was following > > > mdrun -v -deffnm md >& md.job & > > now what comment is true for restart? > I've recently started working with the gromacs and i am not professional > thank you and best wishes for you > > ----- Forwarded Message ----- > From: Mark Abraham <mark.j.abra...@gmail.com> > To: Mahboobeh Eslami <mahboobeh.esl...@yahoo.com>; Discussion list for > GROMACS users <gmx-users@gromacs.org> > Sent: Tuesday, September 17, 2013 12:23 PM > Subject: Re: [gmx-users] How to restart the crashed run > > > You named them last time you ran mdrun, either explicitly or with > -deffnm. Do the same. > > Mark > > On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami > <mahboobeh.esl...@yahoo.com> wrote: >> when i use following omment for restart >> >> mdrun -s md.tpr -cpi md.cpt >> i get following error >> >> Output file appending has been requested, >> but some output files listed in the checkpoint file md.cpt >> are not present or are named differently by the current program: >> output files present: md.log >> output files not present or named differently: md.trr md.edr >> >> >> but i have md.trr and md.edr in my folder. >> >> thank you so much >> >> >> ----- Forwarded Message ----- >> From: Mark Abraham <mark.j.abra...@gmail.com> >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Sent: Tuesday, September 17, 2013 11:22 AM >> Subject: Re: [gmx-users] How to restart the crashed run >> >> >> Hi, >> >> Please keep discussion on the mailing list. >> >> If you have a .cpt file that is not called state.cpt, then you must >> have asked for the checkpoint file to be named md.cpt in your original >> mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the >> default filename (and mostly there is no reason to change that). >> Simply use md.cpt, now that you have it :-) >> >> Mark >> >> >> On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami >> <mahboobeh.esl...@yahoo.com> wrote: >>> I have md.cpt but I don't have restart my run >>> What is the purpose of the state.cpt file? >>> thank you so much >>> >>> From: Mark Abraham <mark.j.abra...@gmail.com> >>> To: Mahboobeh Eslami <mahboobeh.esl...@yahoo.com>; Discussion list for >>> GROMACS users <gmx-users@gromacs.org> >>> Sent: Tuesday, September 17, 2013 9:36 AM >>> Subject: Re: [gmx-users] How to restart the crashed run >>> >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests >>> the 3.x-era restart strategy when checkpoint files are unavailable. >>> But if you simply have no output files, then you have no ability to >>> restart. >>> >>> Mark >>> >>> On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami >>> <mahboobeh.esl...@yahoo.com> wrote: >>>> hi my friends >>>> >>>> please help me >>>> >>>> i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near >>>> the end of the simulation >>>> How to restart the crashed run? >>>> >>>> in the gromacs.org following comment has been proposed >>>> >>>> mdrun -s topol.tpr -cpi state.cpt >>>> >>>> but i don't have state.cpt in my folder. >>>> >>>> I need urgent help >>>> Thank you very much >>>> >>>> -- >>>> 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-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-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-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-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
