Re: AMBER: Running on MPI

From: Carlos Simmerling <>
Date: Mon, 04 Oct 2004 07:37:18 -0400

it would be much easier to help if you tell us exactly what sander does
and if you get any error message or output file.

does the single processor (non-mpi) sander work?

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

wish_71 wrote:

>Hi, Dear all amber users,
>Recently, I installed AMBER7 in 32-CPU PC-cluster in the Red Hat Linux system.
>The correct running format of Sander is as following???
>mpirun -np 4 sander -O -i -o md.out -p -c md.crd -r md.restrt -ref md.crd
>When I input above words, the sander does not work? Then how about the correct running format?
>Looking forward to any help!
>Thanks a lot in advance!
>Best wishes,
>Wu Yingliang
>College of Life Science
>Wuhan Univeristy
>Wuhan, China
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Received on Mon Oct 04 2004 - 12:53:00 PDT
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