[MMTK] Langevin dynamics using CalphaForceField

Geoff Rollins geoffrey.rollins at ucsf.edu
Sat Sep 6 06:21:52 UTC 2008


On Sep 5, 2008, at 7:35 AM, Konrad Hinsen 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

Thanks,
Geoff




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