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: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
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La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Sun Nov 10 2002 - 14:35:16 PST
