title: A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes.
abstract: In order to extend the time and distance scales of molecular dynamics simulations, it is essential to create accurate coarse-grained force fields, in which each particle contains several atoms. Coarse-grained force fields that utilize the Lennard-Jones potential form for pairwise nonbonded interactions have been shown to suffer from serious inaccuracy, notably with respect to describing the behavior of water. In this paper, we describe a coarse-grained force field for water, in which each particle contains four water molecules, based on the Morse potential form. By molecular dynamics simulations, we show that our force field closely replicates important water properties. We also describe a Morse potential force field for alkanes and a simulation method for alkanes in which individual particles may have variable size, providing flexibility in constructing complex molecules comprised partly or solely of alkane groups. We find that, in addition to being more accurate, the Morse potential also provides the ability to take larger time steps than the Lennard-Jones, because the short distance repulsion potential profile is less steep. We suggest that the Morse potential form should be considered as an alternative for the Lennard-Jones form for coarse-grained molecular dynamics simulations.
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Illinois 60616, Department of Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801.
authors.forename: See-Wing
authors.initials: SW
authors.lastname: Chiu
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Illinois 60616, Department of Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801.
authors.forename: H Larry
authors.initials: HL
authors.lastname: Scott
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Illinois 60616, Department of Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801.
authors.forename: Eric
authors.initials: E
authors.lastname: Jakobsson