Re: AMBER: MPI script

From: Thomas Cheatham III <>
Date: Fri, 13 Jul 2007 16:19:37 -0600 (Mountain Daylight Time)

> In submitting a job to run on AMBER, this is the script I
> used:

Your PBS script looks OK except for a couple of things...

> mpirun -np 4 $AMBERHOME/exe/sander -O -i -p ...

You are referencing "sander" which normally refers to the sequential
version (so it would effectively just run on one node). Perhaps you mean
to run sander.MPI (or perhaps sander.MPI was renamed to sander).

> (19): invalid reference to variable in NAMELIST input, unit 5, file

This states that you have a problem with your "mdin" file, something in
there that is not recognized as a AMBER input option. If you post the
mdin file, we may be able to figure out, otherwise, carefully check to see
that none of the keywords are misspelled or anything...

-- tec3
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Received on Sun Jul 15 2007 - 06:07:44 PDT
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