Re: AMBER: replica exchange hangs

From: Carlos Simmerling <>
Date: Wed, 01 Mar 2006 13:37:40 -0500

very strange. If I can get your inputs I'd like to run it under
Amber9, I've changed a lot of the REMD code and I hope it would
solve this.

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

Academic year 2005 address:
Brookhaven National Laboratory
Computational Science Center
Upton, NY 11973

Peter Varnai wrote:

>Dear Amber-group,
>A 16 replica exchange simulation (with LD and GB) ran successfully
>over 10000 exchanges every 1 ps (including several restarts). However
>after a certain successful exchange the code hangs: cpu used and no
>output written. This behaviour was seen on multiple platforms,
>compilation, in batch vs interactive modes. I restarted it from the
>last successful rst files and tried different random seeds/exchange
>frequency and finally attempted exchange every step (1 fs) and checked
>the final, written output files but nothing unusual with coordinates
>or energies.
>I would welcome any suggestion what might be wrong with it.
>Thanks for your help.
>Best regards,
>The AMBER Mail Reflector
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Received on Sun Mar 05 2006 - 06:10:12 PST
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