Hi Justin, Except for cpt i think rest of the command should be alright.
For outputting cpt file and using it for extending runs, i must have used -cpo and not -o flag. 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 15:05 To: Discussion list for GROMACS users Subject: Re: [gmx-users] check point file corrupted - umbrella sampling Poojari, Chetan wrote: > Hello Justin, > > Thank you very much for your reply. > > I must hav used -cpo 0.cpt instead of -o 0.cpt. > Are you saying the commands shown below are wrong? Using "-cpo 0.cpt" is indeed the correct approach. -Justin > > 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 > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > -- ======================================== 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 -- 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? 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