Thanks Justin !! But my state_prev.cpt file shows $gmxcheck -f state_prev.cpt
Checking file state_prev.cpt # Atoms 186864 Last frame -1 time 9346.700 Item #frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Here also the time is greater than the .trr file. Cant understand how to overcome it. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:02 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Chandan Choudhury wrote: > >> 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. >> >> > Right, it will start from whenever the checkpoint was written. You should > also have a state_prev.cpt that is a backup in case this type of thing > happens; it may help. Regardless, with a 36-GB .trr file, the -append > option will not work. Leave it out and use trjcat later. > > -Justin > > 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<mailto: >> 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 >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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/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