Re: [AMBER] how to understand disappearing atoms no contribution to DVdl

From: David A. Case <>
Date: Wed, 23 Feb 2011 09:52:53 -0500

On Wed, Feb 23, 2011, Junjian Miao wrote:
> in the amber10 manual, there is a sentence “It means that any bond,
> angle, dihedral or 1-4 term that involves at least one appearing or
> disappearing atom is not scaled by λ and does not contribute to
> <∂V/∂λ>”(p106), how to account for it?

Can you phrase your question more explicitly? What is the "it" that you want
to "account for"?

In your attachment, the bond, angle and dihedral terms in the second and third
lines are not lambda-dependent; the terms on the first line are scaled
linearly with lambda, and term in the box uses a special, "softcore"

...hope this helps...dac

AMBER mailing list
Received on Wed Feb 23 2011 - 07:00:03 PST
Custom Search