Generalized Born solvation models supported by NAMD

From: Thomas Evangelidis (
Date: Fri Jul 29 2016 - 10:26:13 CDT


I know NAMD supports the GB-OBC models I and II for implicit solvent
simulations [1], which correspond to AMBER parameter igb=2 and igb=5
values, respectively. One simply has to change GBISDelta, GBISBeta, and
GBISGamma values to switch between these two models. Is it necessary to
activate surface tension (NAMD parameters "sasa on" and "surfaceTension
0.0072", as in AMBER)?

Also, is it possible to use with NAMD the older GB-HCT model [2], which
corresponds to AMBER parameter igb=1?

thanks in advance,

​[1] Onufriev, A.; Bashford, D.; Case, D. Exploring protein native states
and large-scale conformational changes with a modified generalized Born
model. Proteins, 2004, 55, 383–394.
[2]​ Tsui, V.; Case, D. Molecular dynamics simulations of nucleic acids
using a generalized Born solvation model. J. Am. Chem. Soc., 2000, 122,

Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic


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