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Journal of Chemical Physics, submitted (2011) (2011)

The String Method on collective variables finds minimum free energy paths (MFEP) between metastable states of a molecule. This requires choosing 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 extract- ing collective variables from low frequency instantaneous normal modes projected onto dihedral angles. We have applied this method to characterize isomerization transitions of alanine dipeptide. The algorithms we have developed are general and can be readily applied to larger systems. We also show that these collective variables simplify the String method and make it numerically more robust.

This paper shows how to build reaction coordinates automatically using low frequency normal modes, and uses these coordinates in the String method to find minimum free energy paths between two conformations of a protein.

This study showed how to automatically compute collective variables for the String method to compute reaction paths. Executables, input files, and analysis scripts are provided for an example of isomerization transitions in alanine dipeptide.


The software applications can be used to reproduce Figures 5-7 of the publication. The method could be adapted for other proteins without much change, except in the configuration files.

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