AMBER Archive (2009)

Subject: RE: [AMBER] PDMED

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 09 2009 - 01:35:25 CDT

Hi Catein,

> Thank you. Installation in our supercomputer is nice. Could you mind
> to let me know how can we use pmemd? Are there any step by step
> instruction on how to run a pmemd calculations? Can we use the same
> prmtop, inpcrd and in files for pmemd? Should we call up the
> calculation with $AMBERHOME/pmemd ..... command rather than
> $AMBERHOME/sander ..... commands?

PMEMD is a complete drop in replacement for sander.MPI. Just replace

$AMBERHOME/exe/sander.MPI

with

$AMBERHOME/exe/pmemd

all other command line arguments, input files, output files etc will be the
same.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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