[gmx-users] Re: Extending run using tpbconv and mdrun

Erik Marklund erikm at xray.bmc.uu.se
Thu Apr 19 13:03:34 CEST 2012

-maxh is not about extending the simulation. What you do is that you start a 10 ns simulation that write checkpoints at regular intervals. With the -maxh option you instruct mdrun to run a certain amount of time (e.g. 8 hours overnight) and the next time you start the simulation (e.g. the next evening) it will continue from the last checkpoint file. Thus there is no need for dividing your simulation in 2 ns chunks with separate tpr/trr/xtc/edr/log files, for mdrun will append further output to the existing files.

If you have already completed a 2 ns simulation and wish to extend it further I think that extending it to 10 ns and use the strategy outlined above is easier than splitting it into more parts. Note how unintuitive it is with a bunch of tpr files named protein_previous, protein_another, etc. There is little point in manually keeping track of what file belong to what part of the simulation when mdrun is capable of continuing form a cpt file ans appending the output to existing files.

19 apr 2012 kl. 12.02 skrev D_Roy:

> Hi, 
> My computer can only manage 2ns in 8 hours. I need a 10ns of simulation run
> for which I have to break up the simulation. You have mentioned using maxh
> option to run the simulation. I read in the mailing list it can be used to
> extend a simulation run and is a better option than tpbconv.
> Can you help me out as to how to use the maxh option to extend the
> simulation?
> I have performed the first step with mdrun -v -deffnm protein_previous
> Now how will I extend this?
> 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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