Which version of MMPBSA.py are you using? The version released with Amber 11
or the version currently available on the tutorial website?
-Bill
On Thu, Oct 28, 2010 at 4:48 PM, zhihong ke <ebelleke.gmail.com> wrote:
> 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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Oct 28 2010 - 14:00:06 PDT
