Re: belly and ivcap conflict in gibbs

From: David A. Case <>
Date: Sun 10 Nov 2002 14:35:16 -0800

On Sat, Nov 09, 2002, sxzheng wrote:

> I met the question that I can use belly=1 , ivcap=0 and fcap=1.5 in sander
> to do a equlibrium.When I take the rst file to gibbs calculation, the
> system's temperature will increase rapidly and stops for torcoon and shaken(
> Routine TORCON internal constraints failed to converage within 1000
> iterations.

It's safest to do equilibration in gibbs if you are planning to do a free
energy simulation there. gibbs and sander have diverged enough that not
all options are compatible.

Also, try using restraints (ntr=1) rather than belly to see if that helps.

..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
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Received on Sun Nov 10 2002 - 14:35:16 PST
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