[MMTK] Normalized distance vectors

Lars Skjærven larsss at gmail.com
Thu Aug 15 10:10:02 UTC 2013


Dear MMTK users,
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.

It seems to me that to reproduce the ANM-modes, the vectors should not be
normalized, in contrast to the calpha-ff. This seems compatible when I try
to find my way through the source code of both MMTK and ProDy (ANM), but
the rationale for this is a bit unclear. Or am I on totally wrong tracks
here?

All best,
Lars
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