It may be a case. You can rename the files to what they were and try again. Since here, the error simply implies the files are renamed or missing.
Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India On Thu, May 26, 2016 at 4:46 PM, sun <sun.i...@gmail.com> wrote: > Yes > In my case it was state.cpt and used the following command after > generating .tpr: > gmx mdrun -v -s next1.tpr -cpi state.cpt > > Has it anything to do with trajectory or log files generated in 100 ns > case? I have renamed the .trr and .xtc files generated for 100 ns > simulation. > > Sent from my iPhone > > > On 26-May-2016, at 4:43 pm, SAPNA BORAH <sapnauser...@gmail.com> wrote: > > > > Well that's kinda new i must say. Can you please paste the entire command > > you have used. I think you have mis-named the file :). > > > > By previous.cpt, I mean your last/previous checkpoint file of the > > simulation run, that will be state.cpt in your case.. Hope you have > > mentioned that. Ignore if you have :) > > > > Sapna Mayuri Borah > > c/o Dr. A. N. Jha > > Research student > > Tezpur University, > > India > > > >> On Thu, May 26, 2016 at 4:38 PM, sun <sun.i...@gmail.com> wrote: > >> > >> Hello Sapna > >> I tried adding previous.cpt but the following the following error > appears: > >> "One out of the 4 files is either missing or renamed" > >> > >> > >> > >> Sent from my iPhone > >> > >>> On 26-May-2016, at 4:35 pm, SAPNA BORAH <sapnauser...@gmail.com> > wrote: > >>> > >>> Hi!! > >>> > >>> After converting the tpr, while initiating mdrun, try adding the > previous > >>> cpt file as well.. > >>> > >>> mdrun -s next.tpr -cpi previous.cpt > >>> > >>> Thanks! > >>> > >>> > >>> Sapna Mayuri Borah > >>> c/o Dr. A. N. Jha > >>> Research student > >>> Tezpur University, > >>> India > >>> > >>>> On Thu, May 26, 2016 at 4:31 PM, sun <sun.i...@gmail.com> wrote: > >>>> > >>>> Hello > >>>> I started a 100 ns ns pro-lig simulation which was terminated > accidently > >>>> at 53.33 ns. Then I restarted simulation with checkpoint file and > >>>> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr > files > >>>> which were generated for 53.33 and 100 ns data reapectively and log, > trr > >>>> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt, > >>>> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i gave > >> the > >>>> following commands: > >>>> gmx convert-tpr -f md_0_1.tpr -extend 200000 -o next1.tpr > >>>> and > >>>> gmx mdrun -v next1.tpr > >>>> > >>>> But, the mdrun started from initial step and time 0.00. That means > >>>> simulation is starting from begining and not after 100 ns to 200 ns. I > >> am > >>>> confused if i am using the right .tpr file or shall I use checkpoint > >> file. > >>>> Same results are obtained when i used next.tpr instead of md_0_1.tpr. > >> When > >>>> i used checkpoint files (all three files in three different steps) the > >>>> simulation is starting from 53.33 ns. Plz suggest where I am going > >> wrong. > >>>> With Regards > >>>> Suniba > >>>> > >>>> Sent from my iPhone > >>>> -- > >>>> 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. > > -- > > 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.
