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
lfoley.uga.edu
Received on Wed Apr 05 2006 - 23:49:40 PDT
