Re: AMBER: SHAKE poblem with dummy atoms

From: David A. Case <>
Date: Tue, 9 Sep 2003 08:38:49 -0700

On Tue, Sep 09, 2003, Itziar Maestre Asenjo wrote:
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 57 130 131
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.

Since this is indeed a problem with the energetics, you need to look carefully
at the energy values you have. Do some short runs with ntpr=1 (not 1000!) to
see if you can figure out what the problem is. You may have to visualize
your trajectory if there is not obvious problem in the energies themselves.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Tue Sep 09 2003 - 16:53:01 PDT
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