[gmx-users] rerun problem

[Tanping Li]

But according to my experience, if you use pme,
different number of processors will give you different
coulomb long-range even if you use the totally same
trr file. I am suffering this point. Does any one else
has the same experience?

tanping


--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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 
> > Neda
> > 
> > 
> > 		
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> -- 
> David.
>
________________________________________________________________________
> 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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