AMBER Archive (2007)

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

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Tue Jul 03 2007 - 12:14:29 CDT


> 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.
Thanks,
Holly

--
Department of Physics, University of Alberta
Edmonton CANADA

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