title: Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit.
abstract: A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the "tip effect" in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.
authors.affiliation: Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. hlwood@nih.gov
authors.forename: H Lee
authors.initials: HL
authors.lastname: Woodcock
authors.forename: Wenjun
authors.initials: W
authors.lastname: Zheng
authors.forename: An
authors.initials: A
authors.lastname: Ghysels
authors.forename: Yihan
authors.initials: Y
authors.lastname: Shao
authors.forename: Jing
authors.initials: J
authors.lastname: Kong
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
mesh_terms: D002073:Butanes / Q000737:chemistry; D003510:Cyclohexanes / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009038:Motion; D010455:Peptides / Q000737:chemistry; D011789:Quantum Theory; D013816:Thermodynamics; D014732:Vibration
chemical_list: D002073:Butanes; D003510:Cyclohexanes; D010455:Peptides; C506365:Cyclohexane; C046888:butane