Changing the Potential Energy Function

From: Hok-Hei Tam (
Date: Thu Feb 04 2010 - 22:08:41 CST

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
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

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