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

From: Jason Swails <>
Date: Fri, 5 Oct 2012 10:27:42 -0400

On Fri, Oct 5, 2012 at 7:48 AM, Carlos Simmerling <> wrote:

> pmemd can be used on more cores than sander for GB calculations. not just
> better scaling, but sander has hard limits of # cores for GB (1 per
> residue, I think).

True, sander has that limit since the bond/angle/dihedral workload is
broken up by residue, but pmemd has a similar, but slightly smaller, limit
in place (10+ atoms per core or pmemd will complain). The main GB loop is
still parallelized exactly the same way in both programs, and so they even
scale similarly.

In fact, I think the *fastest* GB routines in Amber are in NAB*, since it
has a nonbonded pairlist for GB (although I can't speak on the parallel

All the best,

*Fastest CPU routines

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Oct 05 2012 - 07:30:02 PDT
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