Re: Gibbs stops after a finite number of window runs

From: David A. Case <>
Date: Sat 1 Feb 2003 13:11:43 -0800

On Sat, Feb 01, 2003, Seongeun Yang wrote:
> I'm doing perturbation calculations using gibbs with the following input.
> But after calculating only 35 windows, gibbs finishes running for both
> FEP and TI.
> I can't see any reason for this finite number of windows.


> almda = 1.0, almdel = 0.02,
> almdl0 = 0.01,
> isldyn = -2, idifrg = 0,

By setting isldyn=-2, you are asking for "dynamically modified windows".
This means that the number of windows is not determined in advance, but
is adjusted by the program. The value of almdel is ignored.

You should look at the values of the lambdas that were used. If nothing
went wrong, they should roughly (but not uniformly) span the range from
1 to 0. I'm not sure why you were worried that there were "only" 35
windows...this is actually quite a respectable number.

If you want to specify in advance the number of windows, set isldyn=-3.

..hope this helps....dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Sat Feb 01 2003 - 13:11:43 PST
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