Re: Dihedral scan in NAMD?

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Jun 23 2008 - 10:47:07 CDT

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
>
>
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