[gmx-users] About the binary identical continuation by restarting from the checkpoint file

GuoGuangjun guogj at hotmail.com
Mon Feb 23 04:22:19 CET 2009

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. 
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.

Thanks in advance.
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