Re: amber-developers: No DV/DL values at clambda=1 for vdW pert

From: Ilyas Yildirim <>
Date: Fri, 10 Mar 2006 08:07:33 -0700

I am not sure how this works with icfe=1, but when I set icfe=2, for
lambda=0 and lambda=1, the dv/dl values are not printed out. They are
analytically zero. When I run with lambda=0.05 or lambda=0.95, I am
getting dv/dl values, but they are close to zero. I am doing a dummy to
hydrogen and hydrogen to dummy transformations in the TI calculation. So,
I am guessing that the same thing happens with icfe=1 when lambda=1,
because analytically it is zero.

On Fri, 10 Mar 2006, B. Lachele Foley wrote:

> I've done van der Waals perturbation in Amber 8 and Amber 9.
> My issue (below) happens in both. I want to know if it can
> change for Amber 9.
> The context, here, is disappearing atoms in an explicit box of
> water by first turning off charges and then by turning off the
> van der Waals.
> When I run the charge perturbation, I get DV/DL values printed
> in the output file for all values of clambda.
> When I run a vdW perturbation, I get DV/DL values printed in
> the output file for all values of clambda except 1. There
> should be a value at 1, even if it's zero. When I say not
> printed, I mean that "grep DV\/DL blah_1.000.o" yields nada.
> Do you know why the values aren't printed? Can they be
> printed? I'm using klambda=6, if that's important.
> You'd never notice this with quadrature. For my systems,
> though, having endpoints seems to improve accuracy.
> :-) Lachele
> B. Lachele Foley, PhD, '02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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Received on Wed Apr 05 2006 - 23:49:40 PDT
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