[AMBER] Meaning of setting gbsa=0 in generalized Born calculations

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Fri, 5 Oct 2012 00:01:50 -0400

Hi all,

According to the amber manual the free energy of solvation has a
electrostatic and a non-electrostatic part, the non-electrostatic part of
which is calculated as a product of a experimentally obtained
proportionality constant times the solvent accessible surface area.

So if I set gbsa=0, will the non-electrostatic portion not be calculated?

I am specifially asking this because pmemd doesn't support gbsa>0 and when
I use sander, the calculation is so very slow. When I have gbsa=0 and run
with pmemd it is very fast but I wanted to make sure how accurate it would

Thank you

Sajeewa Dewage
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Received on Thu Oct 04 2012 - 21:30:02 PDT
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