Hi JIom, > On 29 Apr 2015, at 11:50, gromacs query <gromacsqu...@gmail.com> wrote: > > Dear All, > > mdrun is not giving any error about missing cpt file. It runs using tpr > from initial time zero. Sometimes my job get killed and I need to use cpt > file in some script but if cpt is not found my job starts running from zero > time in tpr file which is harmful as it consumes my processors to run job > again from time zero. I would expect it should get killed with error if > some cpt file is not found. My command line in script goes like this: This is not a bug but a feature :)
From mdrun -h: "A simulation can be continued by reading the full state from file with option -cpi. This option is intelligent in the way that if no checkpoint file is found, Gromacs just assumes a normal run and starts from the first step of the .tpr file.” > > mdrun_mpi -s dyn.tpr -x dyn.xtc -e dyn.edr -c dyn.gro -g dyn.log -cpi > previous.cpt -cpo dyn.cpt > > In this case if provious.cpt is not found mdrun still runs my job but > starting from zero time. Why it should not get killed complaining about > missing previous.cpt file? > > Do I need to force something? If you specifically only want to run an MD if a .cpt file is found, you could do that, e.g. in bash with: if [ -f previous.cpt ] ; then mdrun … else printf “No checkpoint file found.” fi Carsten > > Thanks, > JIom > -- > 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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.