Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling

From: David A Case <>
Date: Tue, 23 Oct 2012 08:26:28 -0400

On Tue, Oct 23, 2012, Anselm Horn wrote:
> In the very first e-mail "biolabcs" asked whether a cis/trans transition
> can be observed using MD.
> As a first answer I'd say: No, it cannot.
> Cis/trans isomerisation involves electronic transitions that may be
> described by QM methods, whereas in classical force fields explicit
> energy terms exist that try to ensure planarity of double-bond systems.

Molecular mechanics force fields don't allow bonds to break, but do allow
torsion angles to change. Rotations about double bonds have high barriers
(typically 30 kT or more), but the barriers are not infinite, and cis/trans
transtions certainly *can* take place. Unwanted transtions can be found in
initial equilibrations (where there may be very strong forces), or during
high-temperature runs (as in REMD), or indeed with *some* probabilty at any


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Received on Tue Oct 23 2012 - 05:30:04 PDT
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