AMBER Archive (2004)

Subject: AMBER: <dV/dL> fluctuations in TI

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Wed Nov 17 2004 - 05:39:01 CST

Experience is what you get when you don't get what you
want.

                      -- Dan Stanford--

Dear all,

Im using TI within sander in order to compute the free
energy between two enantiomeric complexes, via an
intermediate molecule that is transformed into R or S by
mutation of the apropriate group into dummy atoms.
Im using 12 points for Gaussian Quadrature, the same
points recomended in the manual, to perform data
collection for <dV_dL>. I also set klambda=6 and use 20 ps
for equilibration period and 30 ps for collect averages.
When I look at the results of dV_dL for the fisrt 5 points
the behavior is good, having relatively small fluctuation
dor dV_dL, but for the last points I have very larges
fluctuations for <dV_dL>.
My question is: How can I reduce the large fluctuation for
the last points? Should I use more equilibration time? Or
changing the value of klambda to 4 or 5?

Thanks to all in advance.

Regards

Nelson Fonseca
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