Hi, You'll need to manually append the files using trjcat and eneconv.
Mark On Thu, 13 Apr 2017 11:56 abhisek Mondal <[email protected]> wrote: > Despite the naming problem will the traj.trr file contain the whole > trajectory information ? The log file says: > Gromacs binary or parallel settings not identical to previous run. > Continuation is exact, but is not guaranteed to be binary identical. > > Probably because I used different number of processors for the same run's > continuation. Will my final trajectory file contain all the steps ? If not > then is there any way to join the trajectory information ? > > On Thu, Apr 13, 2017 at 2:32 PM, Mark Abraham <[email protected]> > wrote: > > > Hi, > > > > Your second command didn't use deffnm flag, so mdrun interpreted your > > intent as wanting most of the files to be named as the default. The 2016 > > release series refuses to run your second command precisely because of > the > > ambiguity about whether you intend to append, change names, etc. > > > > Mark > > > > On Thu, 13 Apr 2017 08:35 abhisek Mondal <[email protected]> wrote: > > > > > Hi, > > > I was running mpirun -np 1600 mdrun_mpi -deffnm npt on a protein > and > > > outputs were normal but the job crashed as not finished within given > cpu > > > time. > > > > > > Then I used mpirun -np 2048 mdrun_mpi -s npt.tpr -cpi npt.cpt to resume > > the > > > run from previous checkpoint. But, a whole lot of new files are being > > > created. I thought it would be appended in the previous files. > > > > > > Previous files: npt.trr, npt.edr, npt.log, npt.cpt, npt_prev.cpt > > > Files generated after > > > resuming: state.cpt, state_prev.cpt, traj.trr, md.log, ener.edr > > > > > > If I watch the md.log file, it shows DD step as if it has resumed from > > the > > > last run. Did I made any mistakes there ? Am I going to get the whole > > > trajectory information in parts ? > > > > > > I'm using gromacs-4.6.2 > > > > > > Some suggestions will be highly appreciated. > > > > > > Thank you. > > > > > > -- > > > Abhisek Mondal > > > > > > *Senior Research Fellow* > > > > > > *Structural Biology and Bioinformatics Division* > > > *CSIR-Indian Institute of Chemical Biology* > > > > > > *Kolkata 700032* > > > > > > *INDIA* > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > > > > > > -- > Abhisek Mondal > > *Senior Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- > 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 [email protected]. > -- 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 [email protected].
