title: Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.
abstract: Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.
authors: University of Basel, Basel, Switzerland.
authors: A K
authors: AK
authors: Das
authors: University of Basel, Basel, Switzerland. Electronic address: m.meuwly@unibas.ch.
authors: M
authors: M
authors: Meuwly
mesh_terms: D000818:Animals; D006801:Humans; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009169:Mycobacterium tuberculosis / Q000378:metabolism; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: Chemical reaction; Denitrification reaction; Force field; Molecular dynamics; Reactive molecular dynamics