A partial nudged elastic band implementation for use with large or explicitly solvated systems

The nudged elastic band method (NEB) can be used to find a minimum energy path between two given starting structures. This method has been available in the standard release of the Amber9 and Amber10 suite of programs. In this article, a novel implementation of this method will be discussed, in which the nudged elastic band method is applied to only a specific, user-defined subset of atoms in a particular system, returning comparable results, and minimum energy pathways as the standard implementation for an alanine dipeptide test system. This allows incorporation of explicit solvent with simulated systems, which may be preferred in many cases to an implicit solvent model. From a computational standpoint, this implementation of NEB also reduces the communication overhead inside the code, resulting in better performance for larger systems.