[MMTK] Normalized distance vectors

Konrad Hinsen research at khinsen.fastmail.net
Fri Aug 16 06:23:46 UTC 2013

Lars Skjærven writes:

 > I have quick question related to building the Hessian matrix using the calpha- and
 > anisotropic network force fields. The question is whether the distance vectors (for
 > pairs of c-alphas) are normalized prior to the calculation of the second derivatives.

Normalized in the sense of scaling to length one? Why should that be done?

 > It seems to me that to reproduce the ANM-modes, the vectors should
 > not be normalized, in contrast to the calpha-ff. This seems

The only difference between CalphaFF and ANM is how the force
constants are assigned to the pairs. For ANM, it's a step function of
distance, for CalphaFF, a 1/r^6 decay plus a special treatment for
neighbors along the peptide chain.

A few days ago I posted a way to create ENMs by hand in Python
code. You can play with this to verify that there is no difference
between CalphaFF and ANM other than the assignment of force constants.

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: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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