This paper might be of interest [1]. I believe they use gromacs to
calculate electric fields by zeroing out parameters in various parts of the
system, but the principle is the same, and python scripts are included in
the SI.
Also [2] calculates these fields with AMOEBA, which is a little challenging
because of the induced dipoles and such. They made modifications to the
TINKER source code, which are included in the SI along with the analysis
scripts.
-Robert
[1]
http://pubs.acs.org/doi/abs/10.1021/ja403917z
[2]
http://pubs.acs.org/doi/abs/10.1021/jp410720y
On Sat, Mar 15, 2014 at 4:32 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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 - 14:00:02 PDT
