Hello Justin, Thank you very much for your reply.
I must hav used -cpo 0.cpt instead of -o 0.cpt. Kind Regards, chetan ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 20 September 2011 14:44 To: Discussion list for GROMACS users Subject: Re: [gmx-users] check point file corrupted - umbrella sampling Justin A. Lemkul wrote: > > > Poojari, Chetan wrote: >> Hello Chris, >> >> I followed the steps as mentioned in the umbrella sampling tutorial in >> gromacs. >> >> After NPT equilibration step, i did the umbrella simulation runs. >> Below are the commands which i used: >> >> >> grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n >> index.ndx -o umbrella0.tpr >> >> mdrun -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg -s umbrella0.tpr >> -o 0.cpt -c 0.gro -x 0.xtc >> >> >> So, I had 24 such commands in my job submission script (one script i >> had all the grompp command and in other script i had mdrun command) >> for 24 windows, which gave me 24 cpt files. >> >> After the final 24th window run, along with the output names >> specified by me it also outputted default gromacs file names >> state_prev.cpt, state.cpt, md.log, ener.edr. >> >> Please can I know if its necessary to output even log files for these >> 24 windows. >> >> Size of the state.cpt or the other cpt files which i got during npt >> equilibration are 1.2 MB (these cpt files are okie when i do gmxcheck, >> it does not give any error), where as of 24 different cpt files, each >> has file size of 715MB. I had run simulations for 10ns on each window. >> > > Your command specifies "-o 0.cpt" so that's the problem. The file 0.cpt > is not a checkpoint, it is a trajectory. The -o flag produces a .trr file. > More correctly, 0.cpt is not a *single* checkpoint, but rather a trajectory of checkpoints, and though -o can produce such an output, it is typically reserved for .trr output. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
