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

From: Jason Swails <>
Date: Fri, 5 Oct 2012 07:45:19 -0400

On Fri, Oct 5, 2012 at 12:01 AM, Sajeewa Pemasinghe <>wrote:

> 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

pmemd *does* support gbsa>0 (Amber 12). pmemd.cuda does not.

> 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
> be.

pmemd and sander use effectively the same GB code on GPUs. I've noticed
only a marginal speedup using pmemd vs. sander.

If, however, you are referring to the GPU version, then the speedup is
considerable, as you have pointed out.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Oct 05 2012 - 05:00:03 PDT
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