GuoGuangjun wrote: > Hi, All > > > > Before to perform long simulations, I think it is necessary to do > continuous runs. I make several tests > > to check the reliability of restart by using the checkpoint file. First, > I do a 6ps-long run, and then do it > > again by two parts, that is, the first half (3 ps) starts from the same > initial gro file, followed by its > > second half. Here are my operations: > > > > grompp -f 6ps1.mdp -c water.gro -p water.top -o 6ps1.tpr > > mpirun -np 4 mdrun -s 6ps1.tpr -o 6ps1.trr -x 6ps1.xtc -e 6ps1.edr -dlb no > > > > grompp -f 3ps.mdp -c water.gro -p water.top -o 3ps.tpr > > mpirun -np 4 mdrun -s 3ps.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb > no -cpo 3ps.cpt > > > > tpbconv -s 3ps.tpr -extend 3.0 -o 6ps2.tpr -cont > > mpirun -np 4 mdrun -s 6ps2.tpr -o 6ps2.trr -x 6ps2.xtc -e 6ps2.edr -dlb > no -cpi 3ps.cpt -append > > > > The log file tells me----“Restarting from checkpoint, appending to > previous log file.” However, when I > > check the binary files, such as 6ps1.trr and 6ps2.trr, the cmp command > tells me they are not identical.
Use gmxcheck for this test. This will give you either confirmation that you're achieving your objective, or enough information to find out why not. > During these tests, I have turned off the gen_vel, optimize_fft, and > dynamic load balancing (dlb) according > > to Gromacs manual and previous posters. How to obtain the binary > identical continuation? My computational > > environments are Gromacs 4.0.3, lammpi 7.1.4, Redhat Linux, two AMD > Opteron CPUs with dual cores > > in each, 500 SPC water molecules, and the NPT ensemble. Your approach looks right to me. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
