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To generalize to biomolecules, dihedral terms will be
incorporated. Also, in order to take time steps of 100-1000fs, the
bond springs and angle torsions will be constrained. Correction
factors for the angle torsions will be added [94], based on some
analysis of essential MD [3]. The purpose of
constraining is to preserve the structure of the molecule when taking
such long time steps. The method will be tested for ion channel
permeation.
Jesus Izaguirre
2001-07-27