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Repository for string paper

The On-the-fly String Method finds minimum free energy paths (MFEP) between meta-stable
states of a molecule. This requires the choice of a set of reaction coordinates, or collective variables,
along which the transition takes place, which is non-trivial. In this paper we present a method
for automatically extracting collective variables from low frequency instantaneous normal modes
projected onto dihedral angles. We have applied this method to successfully characterize isomer-
ization transitions of alanine dipeptide. The algorithms we developed are general and can be
readily applied to larger systems. We also show that these collective variables simplify the string
method itself.