Hi, Nelson,
Have you checked the structure of the last lambda? As I know, when some
atoms change into dumy (especially for charged residue )without
electrostatic decoupling, very close contact will happen. This pages
maybe helpful: Manual 7, p171-172.
All the best,
Chunhu
----- Original Message -----
From: "Nelson Fonseca" <nfonseca.dq.ua.pt>
To: "Amber Mailing List" <amber.scripps.edu>
Sent: Wednesday, November 17, 2004 3:39 AM
Subject: AMBER: <dV/dL> fluctuations in TI
>
> 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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Received on Thu Nov 18 2004 - 23:53:00 PST
