Re: van der walls-understanding problem

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Tue Aug 26 2008 - 10:05:28 CDT

The cutoff specifies the distance around each atom, i.e. usually a
sphere.
The central atom interacts with all atoms within this sphere, and not
with any atoms beyond the cutoff.
To make the transition from interacting to noninteracting region
smoother, smooth switching functions are applied.
You see, the cutoff distance only specifies the range in which some
interactions are calculated, not the atomspecific interactions
themselves.
I think in The NAMD manual or in one of the tutorials it is described.

eddi

On Aug 26, 2008, at 9:50 AM, Rudra Banerjee wrote:

> i have a rather silly question.
> given that vanderwalls' potential is pair potential,how can we
> define the 'cutoff' and 'switchdist' key in .conf file, which will
> apply same value of cutoff for all atom pair? my feeling is it
> implies all type of atom combination will have same cut-off. isnt
> it physically arguable?
>
> --
> Rudra
> JRF; SNBNCBS
> http://www.bose.res.in/~rudra
>
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=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
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