From: Hongbo Du (hongbodu_at_uark.edu)
Date: Tue Apr 08 2014 - 10:01:01 CDT
The dielectric constant used in the pair interactions in NAMD is the default value of 1. The pair interactions here are different from the dynamics process.
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node74.html. You may adjust the dielectric constant in your configuration file.
You can also use the plugin "NAMD Energy" in VMD to calculate the pair interactions by calling NAMD and you are allowed to set up the dielectric constant there. The exact number quite depends on the environments between ligand and protein.
Please check the paper. "On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi" dx.doi.org/10.1021/ct400065j | J. Chem. Theory Comput. 2013, 9, 2126−2136
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Patrick Chiu [patrick817us_at_yahoo.com]
Sent: Tuesday, April 08, 2014 8:45 AM
Subject: namd-l: the dielectric constant use in pairwise interaction energy calculation of ligand and protein
Would any one tell me about the dielectric constant in the calculation of pairwise interaction energy of ligand and protein?
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