[gmx-users] Extending simulation

[Erik Marklund]

21 okt 2012 kl. 09.22 skrev Shima Arasteh:

> 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! 

It looks like you're mixing up your cpt files. Since you didn't specify a filename for -cpo I bet your simulation produced "state.cpt", so you need to instruct mdrun to use that one as cpt input.

> 
> Isn't it possible to extend a simulation for the second, third,... time?
> 
> 
> What's the problem? Would you please help me?
> 
>  
> Sincerely,
> Shima
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html