Re: Changing the Potential Energy Function

From: Axel Kohlmeyer (
Date: Thu Feb 04 2010 - 22:50:30 CST

On Thu, Feb 4, 2010 at 11:08 PM, Hok-Hei Tam <> wrote:
> Is there a way to modify the potential energy function (not the force field
> parameters) that NAMD uses that does not involve modifying the code and
> recompiling?  I would like to implement a certain PEF for a zinc finger from


> a paper by Sakharov and Lim that includes polarization and charge transfer,
> two effects that help better approximate the binding site.  The polarization
> term involves the distance between the zinc and another ion and the charges
> only.
> The paper in question is "Zn Protein Simulations Including Charge Transfer
> and Local Polarization Effects," and was published in 2005 in JACS.  The
> authors used a "modified CHARMM27 program."
> Thank you,
> --
> Hok Hei Tam
> Dept. of Chemical and Biomolecular Engineering,
> The Ohio State University

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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