[MMTK] Force constants in CalphaFF

Lars Skjærven larsss at gmail.com
Tue Jul 2 14:30:39 UTC 2013


Dear Konrad,
I'm doing a small implementation of the Calpha-FF and NMA. So far I
reproduce the eigenvectors (from MMTK) when using the AnisotropicNetworkFF,
but I'm slightly off when I use the CalphaFF or DeformationFF. I was
therefore hoping you could help me out with some details.

I suspect my error might be related to the force constant calculation. For
the CalphaFF I use equation 17 in your paper "Harmonicity in slow protein
dynamics":
-----
     if( r < .4)
      k = (8.6*(10**5)*r) - (2.39*(10**5))
    else
      k = 128 * r**(-6)
-----
Is this also the implementation in MMTK? (sorry - couldn't find it in the
code). To avoid confusion with the units, I transformed my cartesian
coordiates to nm.

Is there a way I can print these forceconstants for all pairs of ca-atoms
(for my own debugging purpose)? I know the energyAndForceConstants(), but
this gives the entire Hessian matrix..

For the record I'm comparing my modes with EnergeticModes() and
EnergeticMode.rawMode() to avoid temperature scaling and mass-weighting:
-----
universe = InfiniteUniverse(CalphaForceField())
modes=EnergeticModes(universe, temperature=None)
modes.rawMode(6).array
-----


Kind regards,
Lars
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