AMBER Archive (2005)

Subject: Re: AMBER: SANDER BOMB: volume of ucell too big

From: Michael Crowley (crowley_at_scripps.edu)
Date: Thu May 12 2005 - 12:10:20 CDT

Dear Julie,
Please send some more information that will help deciding what to do.
Your system has expanded in at least one direction beyond the limits set
inside sander as worst case expansion. This does not necessarily mean that
there is anything wrong, but there is probably a problem with your system.

The data that would help is:
Is it a non-periodic simulation?
What is the nature of the simulation: Are you trying to unfold a
macromolecule? Is it unfolding?
Is there unrestrained water in a nonperiodic system?
Do you have enough output to show what is happening to the volume of the
simulation if it is periodic?

Sincerely,
Mike

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Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail: crowley_at_scripps.edu
Telephone: 858/784-9290
Fax: 858/784-8688
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