On Fri, 2014-03-14 at 19:48 +0800, Neha Gandhi wrote:
> Is there any alternate method you would know of ?
There is an approach that I can think of. It would help to think of the
electric field at a point charge as simply the force exerted on that
point charge by all other charges in the system divided by the charge of
that point charge. If you can find a way to compute the force vector on
a particular particle due ONLY to the electrostatic part of the Amber
potential, you can easily get the electric field using the prescription
above.
The easiest way I can think about doing this is with OpenMM. The
upcoming version of AmberTools will have OpenMM support built into a
stable version of ParmEd that should make analyses like these easier
(once you get over the learning curve, that is). It'll be hard to get a
lot of technical support on this particular project from the Amber
mailing list as there are few(?) OpenMM experts among us.
Good luck,
Jason
P.S. You can start playing with a developmental version of ParmEd by
cloning the github repo: https://github.com/swails/ParmEd
You can use the addljtype action in the ParmEd API to zero-out all
Lennard-Jones terms in your system and then get the energies and forces
from the OpenMM API specifying _just_ the nonbonded energy group. You
can see the AmberTools manual for instructions on using the ParmEd API
and the OpenMM website for documentation on the OpenMM Python API. The
docstrings in ParmEd also have helpful documentation and the code may
serve as useful examples of what you can do.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 14 2014 - 06:00:03 PDT
