[gmx-users] Continue running in Gromacs 4.0

xuji xuji at home.ipe.ac.cn
Sun Feb 8 03:32:42 CET 2009


Hi all:

First I should say sorry for all the people who have read this thread for the same following content as the thread
with wrong title I wrote yestoday "cCntinue running in Gromacs 4.0" .

In Gromacs-4.0 manual it's said that we only need the check point file to continue the simulation.
I have a simulation with 16 threads at two nodes. I used the following command to run the simulation:

mpiexec -machinefile ./mf -np 12 mdrun -v -cpo dppc_md_1.cpt -cpt 60 -s dppc_md.tpr -o dppc_md.trr -x dppc_md.xtc -c dppc_md.gro -g dppc_md.log -e dppc_md.edr >& dppc_md.job &

but when I continue the simulation with 

mpiexec -machinefile ./mf -np 12 mdrun -v -cpi dppc_md_1.cpt -cpo dppc_md_2.cpt -cpt 60 -append -s dppc_md.tpr -o dppc_md.trr -x dppc_md.xtc -c dppc_md.gro -g dppc_md.log -e dppc_md.edr >& dppc_md.job &

The mdrun program stopped with "No previous checkpoint file present, assuming this is a new run."

I checked the files in the simulation directory, there is also a file called "dppc_md_1_prev.cpt".
So I try the file called "dppc_md_1_prev.cpt" with 

mpiexec -machinefile ./mf -np 12 mdrun -v -cpi dppc_md_1_prev.cpt -cpo dppc_md_2.cpt -cpt 60 -append -s dppc_md.tpr -o dppc_md.trr -x dppc_md.xtc -c dppc_md.gro -g dppc_md.log -e dppc_md.edr >& dppc_md.job &

I also got "No previous checkpoint file present, assuming this is a new run."	
So can someone tell me what's wrong with my method and how can I continue a simulation in Gromacs-4.0?

Appreciate any help in advance!
 				

        xuji
        xuji at home.ipe.ac.cn
          2009-02-08


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