[gmx-users] Extending simulation

Justin Lemkul jalemkul at vt.edu
Sun Oct 21 12:14:25 CEST 2012

On 10/21/12 3:22 AM, Shima Arasteh wrote:
> Hi again,
> I have done mdrun for 5000000 steps (10 ns) and got the results. Then I tried to extend the simulation for another 5000000 steps ( I mean the next 10 ns = 10 to 20 ns ) using this command:
> # tpbconv -s md.tpr -o md.tpr -extend 10000
> # mpirun -np 32 mdrun_mpi -s md.tpr -o md.trr -c md.gro -e md.edr  -g md.log -cpi md.cpt -v
> The simulation started from step 5000000. I got the results as I expected : whole 20ns simulation.
> Then I tried to extend the simulation for another 10ns ( I mean 20ns to 30ns ). So used the last commands again, but the simulation starts from the step 500000. However, I expect it to start from the step 10000000!
> Isn't it possible to extend a simulation for the second, third,... time?
> What's the problem? Would you please help me?

The hazard with using the same file names is that you may have used the wrong 
.tpr file.  Did you use the right md.tpr for the third leg of the job?  Based on 
the commands above, you may have three "md.tpr" floating around, each specifying 
something different.  Note that you can also save yourself some typing with your 
mdrun command:

mpirun -np 32 mdrun_mpi -deffnm md -cpi -v



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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