Re: Dihedral scan in NAMD?

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
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:

http://www.edam.uhp-nancy.fr/ABF/

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 <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
>>
>> Milla
>>
>>
>> ________________________________
>> 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
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                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr
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              Living, shall forfeit fair renown,
              And, doubly dying, shall go down
              To the vile dust, from whence he sprung,
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_______________________________________________________________________

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