Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI

From: Holly Freedman <>
Date: Tue, 3 Jul 2007 11:14:29 -0600

> Take a restart file (or other coordinates) and just run a single step of
> minimization. Do this once with clambda=0.0, and once with clambda = 1.0.
> You should see differences in just whatever has changed (e.g. the vdW terms,
> if that is all you are changing.

Prof. Case,
This was very helpful, but my setup actually seemed OK. So like everone's been telling me, it must just
be a matter of the treatment of VDW repulsion. I hope that with enough steps the average should be
right anyway although the error bar is large.

Department of Physics, University of Alberta
Edmonton CANADA
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Received on Wed Jul 04 2007 - 06:07:34 PDT
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