Re: Forwarded mail....

From: David A. Case <>
Date: Sun 10 Nov 2002 14:40:19 -0800

On Sat, Nov 09, 2002, Narang Manpreet Kaur wrote:

This means that the system used maxcyc iterations (your input parameter, for
the maximum number of energy evaluations) and hence stopped.

I would also like to know what does linmin failure mean.

See the FAQ at the Amber Web page.

> I have also run the sanme molecule in the TIPP3 water minimization is
> fine abut after equilibration when I view its trajectory file the bonds of
> water and the molecle have streched out though there is no bond
> dissociation

Are you running with constant pressure? make sure to equilibrate at constant
volume first. Otherwise, we would need to know more about what you mean by
"streched out"....


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Sun Nov 10 2002 - 14:40:19 PST
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