Hello.
I have installed the MMPBSA.py.MPI and have finished the test in
mmpbsa_py.test.tar.gz downloaded from the tutorial A3.
During the test, when I tried to used 8 processes, it said that the number
of the processes should not be larger than the number of the frames. (there
are only two frames in the test). That means one process was used for either
frame.
However, I found that there is an option "nproc", which could be 3 or any
multiple of 2. My question is :if I set the nproc = 4, then could I use 8
processes for 2 frame? And is this option available for the Nmode
calculation? Is it possible that I use 8 processes for one-single-frame 's
Nmode calculation? And does it help?
On the other hand, it is known that the Nmode is very expensive. In some
literature, a truncated model was used, such as a sphere of 8 Angstrom was
truncated. Is it possible that I just use a task or some function like
IBELLY to provide a residue list, which is allowed to move in the Nmode
minimization and is activated for the Nmode calculation?
Thank you very much!
Zhihong
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Received on Thu Oct 28 2010 - 14:00:05 PDT
