:) Sapna Mayuri Borah c/o Dr. A. N. Jha Research student Tezpur University, India
On Thu, May 26, 2016 at 6:01 PM, sun <sun.i...@gmail.com> wrote: > Allright Sapna. Thank you very much. > > Sent from my iPhone > > > On 26-May-2016, at 4:59 pm, SAPNA BORAH <sapnauser...@gmail.com> wrote: > > > > I would suggest if you want simulation runs with new name, add the > -deffnm > > switch and provide the default name :) > > Saves us from all the trouble to rename the files all over again. > > > > gmx mdrun -v -s next1.tpr -cpi state.cpt -deffnm new > > > > > > Sapna Mayuri Borah > > c/o Dr. A. N. Jha > > Research student > > Tezpur University, > > India > > > >> On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH <sapnauser...@gmail.com> > wrote: > >> > >> 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. > -- > 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.
