From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Mon Jun 23 2008 - 15:21:57 CDT
contrary to what Michel think, a dihedral scan can be achieved in
NAMD using the adaptive biasing force approach, which yields the
associated free energy. For details, see:
Additional restraints can be enforced while scanning the torsion
L. Michel Espinoza-Fonseca a écrit :
> Dear Milla
> As far as I know, you cannot do that with NAMD -at least in a
> straightforward way. Monte Carlo conformational search or a genetic
> algorithm-type of method would be the most suitable for that, but none
> of these methods have been yet implemented in NAMD.
> An alternative (but fuzzy) way to do it would be a set simuleated
> annealing runs, but I'm not sure if this would be the most suitable
> method for a correct dihedral search.
> On Mon, Jun 23, 2008 at 5:06 PM, Kamilla Kopec <ozero22_at_yahoo.co.uk> wrote:
>> Dear NAMD users,
>> Does anyone know a simple way to do a dihedral scan in NAMD? I know how to
>> fix and constrain specific atoms. How would I scan round a chosen dihedral
>> in e.g. 10 degree increments while keeping others fixed?
>> Best Regards
>> Sent from Yahoo! Mail.
>> A Smarter Email.
-- _______________________________________________________________________ Chris Chipot, Ph.D. Equipe de dynamique des assemblages membranaires Unité mixte de recherche CNRS/UHP No 7565 Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97 B.P. 239 Fax: (33) 3-83-68-43-87 54506 Vandoeuvre-lès-Nancy Cedex E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr http://www.edam.uhp-nancy.fr The wretch, concentred all in self, Living, shall forfeit fair renown, And, doubly dying, shall go down To the vile dust, from whence he sprung, Unwept, unhonored, and unsung. Sir Walter Scott _______________________________________________________________________
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