Re: Dihedral Restraints during MD simulation

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Apr 15 2009 - 13:43:18 CDT

Dear Matthieu,

On Wed, Apr 15, 2009 at 12:33 PM, Matthieu Wilhelm
<matthieu.wilhelm_at_ibcp.fr> wrote:
> Hello,
>
> I'm trying to fix a specific dihedral angle in my molecule during MD
> simulation.  It seems to me that I should use TclForces. After
> many unsuccessful try, I'd like to know where I could find example
> scripts to follow.

You should use the extrabonds feature instead, available in NAMD
2.6b1. See http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/8966.html

Cheers,
Leo

>
> Thanks in advance,
> best regards
>
> Matthieu Wilhelm
>
>
>
> --------------------------------------------------------
> Matthieu WILHELM
> PhD. Student
> matthieu.wilhelm_at_ibcp.fr
> Institut de Biologie et Chimie des Protéines
> 7 passage du Vercors, Lyon 69367, France
>

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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