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

From: Holly Freedman <>
Date: Mon, 2 Jul 2007 14:51:12 -0600

 Julien Michel, David Case and David Mobley,
Thank you all for your suggestions. I am worried that the usual issues with VDW decoupling is not my
only problem however because my RMS fluctuations are so high, for example 133kcal/mol at clambda =
0.91802, 11.4kcal/mol at clambda = 0.5. Also I already have klambda = 6 and I am making atoms
disappear only (not appear). That's why I am sure that I must have made some error in the set up of the
perturbation topology file, although I cannot find it. I would guess that there must be major differences
between my perturbed and unperturbed force fields besides the LJ radii which I intended to perturb.
Does anyone know an easy way to compare the perturbed and unperturbed force fields?
Thanks again,

Department of Physics, University of Alberta
Edmonton CANADA
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Received on Wed Jul 04 2007 - 06:07:22 PDT
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