Thanks Lum !!! I had already used the suggestion you mentioned. But my problem is somewhat different. You can go through my previous mail, for more information.
Thanks. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:42 PM, Lum Nforbi <lumngwe...@gmail.com> wrote: > Hi Chadan, > > I have used the two commands below to CONTINUE a run and they worked > fine for me. I am also using gromacs-4.0.5. > > tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr > mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e > wfullmdrun_ener.edr -g md.log -cpi state_prev.cpt -append & > > The first command includes the amount of time by which you want to extend > your run. > The second one just appends the results to your existing files. In this > second command, you are using the new .tpr file you created in the first > command. Use the state.cpt file instead of the state_prev.cpt file in order > to avoid losing time. > > Hope this helps. > > Lum > > > 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 >
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