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

From: Anselm Horn <>
Date: Tue, 23 Oct 2012 09:50:07 +0200

After following the discussion I'd like to add a comment:

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.

However, as it is not clear what the intention of studying the mentioned
cis/trans transistion was it is not possible to provide any further
advise, e.g. using advanced MD methods or resorting to pure QM



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Received on Tue Oct 23 2012 - 01:00:03 PDT
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