[gmx-users] Implicit solvation: nonpolar term?

Justin Lemkul jalemkul at vt.edu
Thu Dec 19 23:59:47 CET 2013

On 12/19/13 5:47 PM, rdwducl wrote:
> Hello,
> I am using GBSA/OBC implicit solvation with an ACE-type approximation for
> the nonpolar term. Having looked at the GROMACS code, it would appear to be
> using the following form for the nonpolar free energy:
> sum_i 4*pi*tension*(R_i + R_s)^2 * (R_i/b_i)^6
> where R_i and R_s are constants (vdw and probe radii), and b_i is the
> conformation-dependent Born radius. The idea is that as solutes come
> together, b_i increases and so the free energy decreases.
> To test this effect, I have written a script that iteratively creates
> configs with the 7 atoms (of type "CH2"):
> (0,0,0)
> (r,0,0)
> (-r,0,0)
> (0,r,0)
> (0,-r,0)
> (0,0,r)
> (0,0,-r)
> and then computes the GB nonpolar energy as a function of r in [0.1,1.0] nm.
> What I'm finding is a /constant/ nonpolar energy, i.e. it is not varying
> with r!
> My input files are below. Am I doing something wrong?

You have 7 atoms that have no bonded geometry, so no matter where you place 
them, the exposed area is constant.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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