Hello,
I'm interested in running some gas phase simulations in AMBER, but would
like to do so on a GPU. At the moment the GPU enabled AMBER is only
available for PMEMD. This means that PME must be enabled, which is not the
usual thing to do for gas phase where one would just have a longer
electrostatic cutoff and not do periodic conditions at all. Someone else
working on the same system has followed the very logical approach of just
making a reasonably large periodic box around the system and then doing PME
with the hope that the box is large enough for the periodic interactions to
be meaningless.
While the above approach should work, it means that you are doing a lot of
PME calculations (calculating the grid and such) that really aren't useful
(since most of that space is a vacuum). I know that in NAMD for instance
one can specify the PME grid spacing to be different than the standard 1
angstrom. This would seem to be the best solution for this problem, to
have a large periodic box and use PME, but to have the PME spacing large
enough that there is really only one grid point and also have the
electrostatic cutoff be high enough that full electrostatics are always
performed such that PME is never actually used. Is there a way to specify
the PME grid spacing in AMBER? I didn't see it in the manual anywhere.
Thanks,
~Aron
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Received on Thu Jan 05 2012 - 13:30:04 PST
