Re: [AMBER] About difference between Sander and Pmemd

From: David A Case <>
Date: Thu, 16 Jun 2011 07:48:01 -0400

On Wed, Jun 15, 2011, Bin Wu wrote:
> Therefore, I wonder simulation results from Pmemd and Sander are supposed to
> be different

Sander and pmemd should give identical results; indeed, the test cases for
pmemd are the same as those for sander, just running a different executable.
But be sure to read section 1.3.4 of the Users' Manual, which discusses
numerical differences between programs.

Check your visualization to be sure there is not some imaging problem. Of
course, it is also possible that you have uncovered some bug. Check the
coordinates of atoms that should be bonded to be sure they have indeed

> or I compiled Pmemd wrong, because the process of Pmemd
> installation is not smooth at all.

Details would help. Compiling pmemd is supposed to be completely smooth
(always is for me). But there are an enormous number of combinations of
compilers and operating systems, so we need to know details of what went

> export TESTsander='../../../../exe/pmemd'; cd chamber/md_engine/dhfr &&
> ./Run.dhfr_charmm.min
> /bin/sh: ./Run.dhfr_charmm.min: Permission denied
> make: *** [test.pmemd] Error 126

This is odd, and I do not recall seeing such a message before. Check the
permissions on the file involved: is it indeed executable? What happens if
you try to execute that script by hand?


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Received on Thu Jun 16 2011 - 05:00:03 PDT
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