AMBER Archive (2004)

Subject: Re: AMBER: scaling 1-4 NB interaction for rings

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 29 2004 - 10:11:02 CDT

On Wed, Sep 29, 2004, j-shimada_at_az.jp.nec.com wrote:
>
> Question regarding scaling 1-4 non-bonded interactions for rings:
>
> I would like to know how the vdw and electrostatic interactions
> are to be scaled for atom pairs, such as a1-a3 and b1-b4
> in 5 and 4-membered rings as depicted in the Figure ?
>
> a1
> / \
> / \
> a5 a2
> | |
> a4---a3
>
> b1---b2
> | |
> b4-- b3
>
> There are two paths connecting these atoms.
>
> 5-mem:
> If a1-a2-a3 is selected, vdw a1-a3 is suppressed.
> On the contrary, if a1-a5-a4-a3 is selected, vdw a1-a3 is scaled by 1/SCNB.
> Which rule should be applied?
>
> 4-mem:
> What about vdw b1-b4?
>

The shortest path "rules": there would be no nonbonded interactions between
a1/a3, or between b1/b4. Any alternative rule would appear to have lots
of problems, and I don't know of any force field that has used it.

...dac
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