Hi Mark !!! Thanks for answering. My query is how do I restart my mdrun because the command nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt -append & will not start from where the trajectory was stopped (i.e; time 9169.500). As this command will continue the simulation from where the cpt file was written.
Any suggestions?? chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 17/02/10 02:52, Chandan Choudhury wrote: > >> Hello gmxusers !!! >> I want to continue my simulation, from where the point where it stopped. >> The gmxcheck on .trr and cpt files are as: >> >> $gmxcheck -f state.cpt >> >> Checking file state.cpt >> >> # Atoms 186864 >> Last frame -1 time 9362.500 >> >> >> Item #frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> $gmxcheck -f 5-10.trr >> >> Checking file 5-10.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 5169.500 >> # Atoms 186864 >> Reading frame 8000 time 9169.500 >> >> >> Item #frames Timestep (ps) >> Step 8395 0.5 >> Time 8395 0.5 >> Lambda 8395 0.5 >> Coords 8395 0.5 >> Velocities 8395 0.5 >> Forces 0 >> Box 8395 0.5 >> >> >> There is a mismatch of time in both the outputs. >> >> The date of modification of both the files as shown are: >> >> Feb 15 19:55 state.cpt >> >> $date -r 5-10.trr >> Mon Feb 15 19:59:56 IST 2010 >> >> The cpt file shows time greater than the trr file. But the time of >> modification of cpt file is less than trr file. >> > > If the simulation stopped catastrophically, then the timestamp could easily > differ, especially if the .cpt is opened, written to and closed > periodically, and the .trr is open continuously. > > > Cannot understand the, >> how to restart the mdrun. And the size of the trr file is 36GB. Can I >> use the append flag in mdrun for gmx 4.0.5. >> > > Search the webpage for suggestions. > > Mark > -- > 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/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/mailing_lists/users.php >
-- 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/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/mailing_lists/users.php