Re: [AMBER] pmemd trajectory for mm_pbsa/gbsa analysis on sander

From: David A Case <>
Date: Thu, 14 Jul 2011 11:05:46 -0400

On Thu, Jul 14, 2011, Sangeetha B wrote:
> I want to run mm-pbsa/gbsa analysis for protein-ligand complexes.
> Since pmemd is faster than sander, I use pmemd (installed on a
> NVIDIA-gpu) for obtaining the MD trajectories and sander for running
> mmpbsa. I want to know whether combining pmemd and sander would affect
> my would be helpful for my work if my query is
> answered...

Subject to the caveats of section 1.3.4 of the Amber11 Users' Manual,
you should have no problem in using either sander or pmemd on the same
project. But be sure the cuda test cases pass, since they ensure that
(subject to numerical precision limitations), you are getting the same
results as for the cpu versions of sander and pmemd.


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Received on Thu Jul 14 2011 - 08:30:02 PDT
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