[MMTK] Langevin dynamics using CalphaForceField

Konrad Hinsen hinsen at cnrs-orleans.fr
Fri Sep 5 14:35:55 UTC 2008

On Sep 5, 2008, at 9:18, Geoff Rollins wrote:

> I'm interested in running Langevin dynamics simulations using the  
> Calpha force field. My understanding is that this force field takes  
> every given configuration to be a potential energy minimum, so that  
> the gradients will be zero at every time step. The test simulations  
> that I've run seem to confirm this since the Calpha's of my protein  
> gradually drift away from each other in all directions.
> I am wondering if there is any simple way to change the default  
> behavior so that only the initial configuration would be a  
> potential energy minimum, i.e. the energy and its gradients would  
> not be zero at every step. Or, if no simple way exists, I'm  
> wondering what sorts of modifications I would need to make in order  
> to achieve this.

Unfortunately your project requires a significant modification to  
CalphaForceField, although it is not a difficult one to make. If you  
want meaningful forces from an harmonic potential, you need to  
provide both the current configuration and a reference configuration  
that defines the minimum of the energy. The current CalphaForceField  
does not have a reference configuration argument at all, so such an  
argument would have to be added. The other modifications (calculating  
the forces) would be rather trivial.

In my opinion it is not a good idea to use the initial configuration  
as a reference. After all, what does "initial" mean in a complex  
script? The first configuration ever used in the script? The first  
one for each dynamics run? Or yet something else?

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
Web: http://dirac.cnrs-orleans.fr/~hinsen/

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