Re: Dihedral scan in NAMD?

From: Chris Chipot (
Date: Mon Jun 23 2008 - 15:21:57 CDT

Dear Milla,

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
of interest.

Chris Chipot

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.
> Cheers,
> Michel
> On Mon, Jun 23, 2008 at 5:06 PM, Kamilla Kopec <> 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
>> Milla
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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
              The wretch, concentred all in self,
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              And, doubly dying, shall go down
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              Unwept, unhonored, and unsung.            Sir Walter Scott

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