Yes!! It works very good!! Thank you, Mark!! On Jul 14, 2015, at 11:39 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> Hi, > > Was that actually your mdrun command line? I think you need > > gmx mdrun -s md_0_2 -deffnm md_0_1 -cpi md_0_1 (with or without -append) > > to actually get appending happening. mdrun does not deduce the names of the > output files from the contents of the checkpoint file. > > Mark > > On Tue, Jul 14, 2015 at 9:47 AM Andrea Spinelli <spinell...@gmail.com> > wrote: > >> Hi Mark, >> in the .log file there are this lines at the start of the extending. >> >> There are: 20587 Atoms >> Charge group distribution at step 500000: 5190 5166 5109 5122 >> Initial temperature: 319.123 K >> >> Started mdrun on rank 0 Sun Jul 12 20:50:29 2015 >> Step Time Lambda >> 500000 1000.00000 0.00000 >> >> >> >> On Jul 14, 2015, at 9:32 AM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> >>> Hi, >>> >>> On Tue, Jul 14, 2015 at 8:10 AM Andrea Spinelli <spinell...@gmail.com> >>> wrote: >>> >>>> @Mark >>>> The .log report works for 2000 ps. >>>> >>> >>> Sure, but you need to look at the bit between 1 ns and 2 ns to find out >>> what happened when you attempted to append. >>> >>> Mark >>> >>> >>>> @Chaban >>>> I not use grompp and the extension not create .trr files. >>>> >>>> What I have to do? >>>> >>>> On Jul 14, 2015, at 3:56 AM, V.V.Chaban <vvcha...@gmail.com> wrote: >>>> >>>>> The no-headache route is: >>>>> >>>>> mv confout.gro conf.gro >>>>> grompp >>>>> mdrun >>>>> trjcat -f *.trr -o fixed.trr >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Mon, Jul 13, 2015 at 6:45 PM, Mark Abraham < >> mark.j.abra...@gmail.com> >>>> wrote: >>>>>> Hi, >>>>>> >>>>>> What did the .log file report about your attempt to append? >>>>>> >>>>>> Mark >>>>>> >>>>>> On Mon, Jul 13, 2015 at 11:18 PM Andrea Spinelli < >> spinell...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> I’m new user of Gromacs and I need extend a simulation of 1000ps. >>>>>>> On Gromacs 5.0.5 I use this command line as tutorial said. >>>>>>> >>>>>>> gmx convert-tpr -s md_0_1.tpr -extend 1000 -o md_0_2.tpr >>>>>>> gmx mdrun -v -s md_0_2.tpr -cpi md_0_1.cpt -append >>>>>>> >>>>>>> It produced the md_0_2.tpr , but when I run rms command to watch the >>>> state >>>>>>> of RMSD, it show only first 1000 ps, not from 0 to 2000 ps. Why? >>>>>>> What is the command I have to use? >>>>>>> >>>>>>> to view rmds I use this command line: >>>>>>> gmx rms -s md_0_2.tpr -f md_0_1.xtc -o rmsd.xvg >>>>>>> >>>>>>> Thanks a lot. >>>>>>> >>>>>>> >>>>>>> Andrea Spinelli >>>>>>> >>>>>>> Please do not print this email unless really need to. >>>>>>> Save paper, save trees, save space, save money - life matters. >>>>>>> >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> Andrea Spinelli >>>> >>>> Please do not print this email unless really need to. >>>> Save paper, save trees, save space, save money - life matters. >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> Andrea Spinelli >> >> Please do not print this email unless really need to. >> Save paper, save trees, save space, save money - life matters. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. Andrea Spinelli Please do not print this email unless really need to. Save paper, save trees, save space, save money - life matters. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
