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

[Mark Abraham]

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