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.
Sincerely,
Shima
________________________________
From: Erik Marklund <[email protected]>
To: Shima Arasteh <[email protected]>; Discussion list for GROMACS
users <[email protected]>
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?
>
>
>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
[email protected]
http://www2.icm.uu.se/molbio/elflab/index.html
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