title: The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials.
abstract: The potential of mean force (PMF) with respect to coarse-grained (CG) coordinates is often calculated in order to study the molecular interactions in atomistic molecular dynamics (MD) simulations. The multiscale coarse-graining (MS-CG) approach enables the computation of the many-body PMF of an atomistic system in terms of the CG coordinates, which can be used to parameterize CG models based on all-atom configurations. We demonstrate here that the MS-CG method can also be used to analyze the CG interactions from atomistic MD trajectories via PMF calculations. In addition, MS-CG calculations at different temperatures are performed to decompose the PMF values into energetic and entropic contributions as a function of the CG coordinates, which provides more thermodynamic information regarding the atomistic system. Two numerical examples, liquid methanol and a dimyristoylphosphatidylcholine lipid bilayer, are presented. The results show that MS-CG can be used as an analysis tool, comparable to various free energy computation methods. The differences between the MS-CG approach and other PMF calculation methods, as well as the characteristics and advantages of MS-CG, are also discussed.
authors.affiliation: Department of Chemistry, James Franck Institute, University of Chicago, 5735 S. Ellis Ave., Chicago, Illinois 60637, USA.
authors.forename: Lanyuan
authors.initials: L
authors.lastname: Lu
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth
mesh_terms: D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry; D000432:Methanol / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D004134:Dimyristoylphosphatidylcholine; D000432:Methanol