Re: [AMBER] sander and pmemd

From: Ross Walker <>
Date: Thu, 26 Apr 2012 06:53:33 -0700

Dear Cao,

> I am a user of AMBER in China. My system is a protein complex with 214
> AA residues. Now I am doing the production phase with sander before
> MMPBSA calculation. But it seems rather slow.
> I noticed that pmemd is an optimized version of sander for speed and
> for parallel scaling. And I have two questions here.
> Q1: As I modeled my system in the first 1ns with sander, whether it is
> proper to turn to use pmemd in the last several ns for the purpose of
> speed?

Yes, this is perfectly reasonable, you can mix and match runs with pmemd and
sander. They read the same input files and write the same output files and
are designed to be completely compatible. The only time you can't do this is
if you are using a method in sander that pmemd does not support in which
case pmemd should quit with an error.

> Q2: Will the results from sander and pmemd be the same? What is the
> difference between the two algorithms?

The algorithms are identical, the results should also be identical within
the limits of machine rounding differences. PMEMD is just more optimized
code and designed to scale better in parallel.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Apr 26 2012 - 07:00:03 PDT
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