Paper Citing NAMD - Abstract
van Hoof, Bram; Markvoort, Albert J.; van Santen, Rutger A.; Hilbers, Peter A. J.
The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10001-10012, AUG 25 2011
Molecular dynamics (MD) simulations are an important tool for studying various interesting phenomena in nature at the molecular level. To allow molecular simulation methods to be applied to larger systems and for longer time scales, coarse grained (CG) models have been developed in which groups of atoms are represented by a single coarse grained particle. In so-called multiscale CG models, an atomistic simulation is coarse grained and subsequently used to derive a CG force field. Existing multiscale methods represent either (parts of) molecules as a single CG particle, or groups of molecules of fluctuating size as a single CG particle. Here, a novel method is introduced to coarse grain an atomistic simulation, the CUMULUS coarse graining method. In this method, CG particles have a unique, fixed composition. This important feature of our coarse graining method, which is not available in the current methods, provides a systematic method to include CG solute particles in solutions of salts in water. Combined with the iterative Boltzmann inversion procedure, our coarse graining method is employed to derive CG force fields for systems containing pure water, sodium chloride solutions, and water-octanol mixtures. It is found that the obtained force fields accurately reproduce the structural information from the atomistic simulations, as measured by the radial distribution functions. Furthermore, we conclude that the obtained CG force fields are transferable to systems of different composition for the systems studied here.
