[gmx-users] rerun problem
David van der Spoel
spoel at xray.bmc.uu.se
Sat Feb 19 09:27:51 CET 2005
On Sat, 2005-02-19 at 00:38 -0800, neda mirsamadi wrote:
> Dear gmx users
> I have simulated a long trajectory before. But by
> mistake I missed part of my energy file in the middle
> of simulation. I need to recalculate energy for that
> part. For that I need to run
> mdrun -rerun *.trr -s *.tpr
> But I have few problems
> 1. I used 4 processors for simulation which I have no
> longer access to that and I have to redo the job on
> single processor and I also used -shuffle option. When
> I use one of my old tpr files it naturally complain
> that job is for 4 processor.
> 2. I want to do calculation exactly for missing part
> and not for entire trajectory.
> Please kindly advice what should be done and how I
> should reconstruct *.mdp file.
You can run in parallel on one processor. If you use LAM, you would
simply go about as usual running mpirun -c 4 mdrun
For MPICH it is similar.
> Thanking in advance
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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