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 pair-wise non-bonded 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 CSJ 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. The Morse potential is implemented in Gromacs, using a rapid table look-up capability available in that simulation package. The table look-up is about 20% slower per time step than the standard Lennard-Jones, but is more than compensated for by the longer time step possible, so that overall simulation times are shorter when using the Morse potential. We suggest that the Morse potential form should be considered as an alternative for the Lennard-Jones form for coarse-grained molecular dynamics simulations. We are working on coarse-grained force fields for amphipathic molecules and for ions, and will provide a progress report on that work in this presentation.