[MMTK] Langevin dynamics using CalphaForceField

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Sep 8 13:39:09 UTC 2008


On Sep 6, 2008, at 8:21, Geoff Rollins wrote:

>> 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.
>
> Does this seem like a reasonable outline of modifications? Have I  
> left anything out?
>
> CalphaFF.py
> 1. add a reference configuration argument to __init__
> 2. in evaluatorTerms, pass the reference configuration to the C code
>
> MMTK_deformation.c
> 1. modify CalphaTerm so that it accepts the reference configuration  
> passed from Python
> 2. add calculation of energy and gradients to calpha_evaluator

That's a good outline.  To prevent improper use, I recommend adding a  
check like

	assert universe is self.reference_configuration.universe

in evaluatorTerms to make sure that you don't apply the force field  
to a universe different from the one for which the reference  
configuration was given.

Konrad.
--
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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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