On 12/19/13 5:47 PM, rdwducl wrote:

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"):


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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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