Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD): Current Status and Challenges.

The fragment molecular orbital-based molecular dynamics (FMO-MD) method simulates the time evolution of a molecular system while calculating the system's conformation-dependent electronic state changes using FMO. This method is implemented in programs such as ABINIT-MP and GAMESS; this article focuses mainly on the former. A preliminary test simulation of a micro-RNA (miRNA) and Benzo-N,N-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine (BzDANP) complex highlights many challenges remaining in applying FMO-MD to biological reactions. Finally, possible solutions to these challenges are presented.