On Fri, Oct 5, 2012 at 12:01 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com>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?
>
Correct.
> 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.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 05 2012 - 05:00:03 PDT
