AMBER Archive (2005)

Subject: Re: AMBER: group-based cutoff

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Aug 10 2005 - 21:53:38 CDT

> I'm curious if a group-based cutoff can be implemented with the AMBER
> force fields (I'm looking at all_amino02.lib in particular). It seems
> that when I try to group atoms together in alanine, for example, I can't
> make charge neutral groups. Are non-neutral groups used? Is a
> residue-based cutoff used at all or is it done based on atom-atom distances?

Why do you want to have a group-based cutoff? Although it was intuitively
thought that having neutral charge groups within the cutoff would lead to
better behavior in MD simulation, this has been shown both in straight
cutoff simulations and also with full treatment of the electrostatics (or
energy/force shift/switch) to not be the case. With highly charged
systems, such as nucleic acids, the worst possible cutoff is a group-based
truncation. Non-intuitively, atom-based cutoff perform better.

There are excellent papers by Steinbach & Brooks that discuss the issues
in detail (including Proteins, 1989; JCC 1994)

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