Roman,
That's interesting ... do you mind sharing with us your data file so
we can reproduce your observation?
All the best,
Ray
On Fri, Sep 16, 2011 at 3:18 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Hello,
> I have a peculiar problem with MMPBSA. I get the same results for GB but different results for PB depending on the number of processors I use.
> Here is the summary:
> The results of gb are identical regardless of the number of processors;
> the results of pb depend on the number of processors:
> gb pb
> 5proc -57.7880 -77.1179;
> 4proc -57.7885 -68.7393;
> 3proc -57.7866 -71.9419;
> 2proc -57.7888 -95.5026
> 1proc -57.7881 -176.9453
>
> These are the final DELTA
> The question is whether this is a problem with the implementation on our computers or a more fundamental problem.
>
> The input file is:
> Input file for running GB
> &general
> verbose=2, strip_mdcrd=1, strip_mask=":WAT",
> entropy=0, startframe=1000, endframe=10000, interval=1000
> /
> &decomp
> idecomp=2, dec_verbose=3,
> /
> &gb
> igb=5, saltcon=0.150
> /
> &pb
> istrng=0.150
> /
>
> and the script (this case for 2 processors) is:
>
> #!/bin/bash
> #PBS -N MM_ALL
> #PBS -j oe -V
> #PBS -q para_std
> #PBS -l select=2:ncpus=1
> #PBS -m e
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/intel/lib/intel64
> export AMBERHOME=/share/apps/amber11
> export PYTHONPATH=/share/apps/python2.6/lib/python2.6/site-packages\:$PYTHONPATH
> MMPBSA="/share/apps/amber11/bin/MMPBSA.MPI"
> PYTHON="/share/apps/python27/bin/python2.7"
> cd $PBS_O_WORKDIR
>
> SUB="mpirun -np 2 $MMPBSA -O -i decomp_tb.in -o decomp_tb.dat -sp ../tryp_bpti_1000.top -cp ../GENR/tryp_bpti_nw.top -rp ../tryp_nw.top -lp ../bpti_nw.top -y ../tryp_bpti_1000.trj -do decomp_tryp_bpti.dat"
> echo $SUB
> $SUB
>
> Thanks for your help
>
> Roman Osman
> roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>
>
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Received on Fri Sep 16 2011 - 21:00:02 PDT
