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.
Guang-Jun
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