AMBER Archive (2000)

Subject: dummy atom as anchor in gibbs ?

From: Terreux Raphael (terreux_at_taloa.unice.fr)
Date: Thu May 25 2000 - 16:53:43 CDT

Dear amber users,

I would measure a variation of the free energy during a biological
process. For this purpose, i plan to use Gibbs modules with iternal
constraints.

Does it possible to use dummy atoms (which stay dummy during all the MD)
constrained with a ibelly, as anchor for the Gibbs constraint ? I
suppose it is possible, but it will may be created artefacts in the
calculation of the variation of free energy ? Does anybody has already
created a Gibbs internal constraint not based on real atom of the system
?

Thanks in advance for your help.

Best regards

raphael terreux 

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TERREUX Raphael

Laboratoire A.S.I Equipe Chimiometrie Modelisation
Universite de Nice-Sophia Antipolis,
Parc Valrose, F 06108, Cedex 2,
NICE, FRANCE

TEL : +33 (0)4 92 07 61 26
FAX : +33 (0)4 92 07 61 25
e-mail : terreux_at_chiminfo.unice.fr
         terreux_at_unice.fr
web    : http://chiminfo11.unice.fr/~terreux/index.htm
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