NAMD Implicit GB Parameters

From: Samuel Bowerman (
Date: Mon Feb 01 2016 - 12:41:03 CST

Hello NAMD community,

I am was hoping somebody could provide insight into how NAMD defines some
parameters for GB simulations. I see from the user manual that atomic
radii are taken from Bondi (1964). How exactly does NAMD apply these
corrections? Is it a direct definition from some table of values, or does
it apply a subraction/addition based upon atom type? I ask this because I
am wary of "double-counting" radii corrections when comparing the results
of NAMD implicit solvent simulations against other ones I have conducted in

More exactly, to do the simulations in Amber, I had to alter the radii
terms in the .prmtop file to mbondi2 (Onufriev, Bashford, and Case, *Proteins
*2004). These parameters are supposedly the best for use with the NAMD
default GB values. If I load this .prmtop into NAMD for a simulation, is
it "double-dipping" into radii corrections by applying a Bondi correction
to the mbondi2 terms, or are they explicitly Bondi radii?

Take care,
Samuel Bowerman
Ph.D. Candidate
Illinois Institute of Technology
Chicago, IL 60616

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