[MMTK] Normal mode analysis problem (model = calpha,cutoff=2.5)

Konrad Hinsen research at khinsen.fastmail.net
Mon Apr 2 06:15:14 UTC 2012

qiancheng shen writes:

 >         Could any one explain me how the matrix was generated?
 > E.g. How to get the first element 287.1434..?

That element is the second derivative of the potential energy with
respect to the x coordinate of the first atom. MMTK has explicit
formulas for the second derivatives of all energy terms, so to
calculate that number, MMTK iterates over the energy terms in exactly
the same way as for calculating the energy, but it adds up the second
derivatives instead.

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

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