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? 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