Thanks Jason :)
On 14 March 2014 20:51, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>
--
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
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Received on Sat Mar 15 2014 - 05:00:03 PDT
