[gmx-users] Extending simulation

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Oct 23 06:37:38 CEST 2012

I have 3 .cpt files in my directory: md.cpt , state.cpt  and state_prev.cpt .
What does each one mean?

I guess I need to use the last cpt in my command # mpirun -np 32 mdrun_mpi -s md.tpr -o md.trr -c md.gro -e md.edr  -g md.log -cpi md.cpt -v
And the md.cpt is not the correct .cpt file in my command.


From: Erik Marklund <erikm at xray.bmc.uu.se>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, October 21, 2012 10:47 PM
Subject: Re: [gmx-users] Extending simulation

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?
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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

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