[gmx-users] Extending run using tpbconv and mdrun

Erik Marklund erikm at xray.bmc.uu.se
Thu Apr 19 11:29:10 CEST 2012


Why not just run the simulation for a limited time (as in real time)? E.g. mdrun ... -maxh 8 if you want it to run overnight for 8 hours. If the computer you are using is not used for other tasks, then there would be no reason at all to spit the simulation in parts. Even if the simulation has not completed the number of steps dictated by the tpr file you can still analyze the results after 2 ns of simulation. It sounds like your strategy creates unnecessary work for you.



19 apr 2012 kl. 10.16 skrev D_Roy:

> Hi,
> I am trying to do a simulation of 10ns of protein in water. Due to the
> limitations in my computer speed, I have decided to break it up in 5 days
> with 2ns run per day.
> For the first 2ns run I have used the commands:
> mdrun -v -deffnm protein_previous
> I went through the gromacs documentation and tried the following method to
> do an extended run of 2ns after the first day:
> tpbconv -s protein_previous.tpr -extend 2000 -o protein_next.tpr
> mdrun -s protein_next.tpr -cpi protein_previous.cpt -cpo protein_next.cpt
> It worked for the first extended simulation giving me the output files:
> confout.gro ; ener.edr ; traj.xtc ; traj.trr ; md.log
> When I try the same steps for 2ns for the third time with the commands:
> tpbconv -s protein_next.tpr -extend 2000 -o protein_another.tpr
> mdrun -s protein_another.tpr -cpi protein_next.cpt -cpo protein_another.cpt
> It start from the beginning. 
>> From the mailing lists, I could guess it may be that mdrun cannot find the
> checkpoint file previous_next.cpt. But the filename is correct. So why is it
> starting from the begining?
> Would appreciate if someone can help me out.
> Thanks.
> Dipankar Roy
> -----
> Research Assistant
> Sikkim Manipal University DE
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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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