AMBER Archive (2003)

Subject: Re: Gibbs stops after a finite number of window runs

From: Seongeun Yang (seongeun_at_ccb.wustl.edu)
Date: Sat Feb 01 2003 - 15:42:42 CST

Thanks for your answer first.
Yeah, I'm trying to do dynamically modified windows calulations.
(I already tried using ISLDYN=-3 for the fixed window calculations.)
With those input parameters, gibbs stopped after calculating from
lambda=1 to lambda=0.85
and the number of windows was 35.
I tried again with the restart file starting from lambda=0.85, but gibbs
stopped again
around when lambda=0.65, and the number of windows was 35 also in this case.
What I'm wondering about is whether this number is already set in the
program as the default
or there is something missing or wrong in my input parameters.

Thanks again,

Seongeun

David A. Case wrote:

>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
>
>
>