if i want to store 10-15 ns .xtc file in a different .xtc file then what should i do. thanking you
On 12/27/18, SHAHEE ISLAM <islamsha...@gmail.com> wrote: > thank you so much. > > On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: >> ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- >> Date: Thu, 27 Dec 2018 16:52:17 +0530 >> From: SHAHEE ISLAM <islamsha...@gmail.com> >> Reply-To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] how to restart a job in grmacs >> To: gmx-us...@gromacs.org >> >>> thank you >>> is the trajectory wil be from 0-15 ns or it will be from 10-15 ns. >>> >>> On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: >>>> ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- >>>> Date: Thu, 27 Dec 2018 16:41:21 +0530 >>>> From: SHAHEE ISLAM <islamsha...@gmail.com> >>>> Reply-To: gmx-us...@gromacs.org >>>> Subject: Re: [gmx-users] how to restart a job in grmacs >>>> To: gmx-us...@gromacs.org >>>> >>>>> thank you so much for your reply. >>>>> -extend 5000 what does it signify.if the time step is 2 fs then by >>>>> simply multiplying these two it will give 10 ns. >>>>> thanking you >>>>> >>>>> On 12/27/18, sp...@iacs.res.in <sp...@iacs.res.in> wrote: >>>>>> ----- Message from SHAHEE ISLAM <islamsha...@gmail.com> --------- >>>>>> Date: Thu, 27 Dec 2018 16:16:18 +0530 >>>>>> From: SHAHEE ISLAM <islamsha...@gmail.com> >>>>>> Reply-To: gmx-us...@gromacs.org >>>>>> Subject: [gmx-users] how to restart a job in grmacs >>>>>> To: gmx-us...@gromacs.org >>>>>> >>>>>>> hi, >>>>>>> i have run a simulation for 10 ns but after 4 ns due to power off >>>>>>> the >>>>>>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi >>>>>>> md_0_10ns.cpt,continue the left simulation.Now after normal >>>>>>> termination of 10 ns how i wll do the next 5 ns simulation after >>>>>>> this >>>>>>> 10 ns. >>>>>>> thanking you >>>>>>> shahee >>>>>>> -- >>>>>>> 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 >>>>>>> >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>> or send a mail to gmx-users-requ...@gromacs.org. >>>>>> >>>>>> Hi >>>>>> You can extend the job by generating a new tpr file >>>>>> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr >>>>>> then restart the job >>>>>> gmx mdrun -s new.tpr -cpi state.cpt >>>>>> This will continue the run from 10 ns. >>>>>> Sunipa >>>>>> ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- >>>>>> -- >>>>>> 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 >>>>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>> or send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> Hi >>>> -extend 5000 means you want to extend 5000 ps or 5 ns extra after 10 >>>> ns. So >>>> your final trajectory will be for 15 ns. >>>> >>>> Sunipa >>>> >>>> ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- >>>> -- >>>> 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 >>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>> or send a mail to gmx-users-requ...@gromacs.org. >> >> It will be from 0 to 15 ns. When you will run the job after extending the >> job it will update the trajectory after 10 ns. >> >> ----- End message from SHAHEE ISLAM <islamsha...@gmail.com> ----- >> -- >> 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.