[AMBER] Progress of calculation in MMPBSA.py.MPI

From: mish <smncbr.gmail.com>
Date: Mon, 3 Jan 2011 13:21:42 +0100


I have a little bit confusion about the entropy calculation using perl
script and MMPBSA.py.MPI
I did some calculation in the past using perl script in just 1 CPU and
calculation took about 30 days on 1 CPU where I re-submitted all those
calculation using MMPBSA.py.MPI in 4CPU (4 threads) and the progress I can
see is much slower than perl. I am not sure about the iterations used in
default input file for sander ( all such files have been deleted from perl
calculation), By default, are we using more cycles in python script than
perl ? After 11 days of calculation for the same number of snapshots (500) I
can see

Starting nmode calculations...
  master thread is calculating 123 frames

  calculating complex for frame number 0
  up to
  calculating complex for frame number 51

If it will run for 500 snapshots like this then I suppose it will take more
time than one CPU ? Can anyone let me know the reason, why is it taking more
time ?

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Received on Mon Jan 03 2011 - 04:30:04 PST
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