Bridging coarse-grained models by jump-in-sample simulations.
We present an efficient method to construct coarse-grained (CG) models from models of finer resolution. The method estimates the free energies in a generated sample of the CG conformational space and then fits the entire effective potential surface in the high-dimensional CG conformational space. A jump-in-sample algorithm that uses a random jumping walk in the CG sample is used to iteratively estimate the free energies. We test the method in a tetrahedral molecular fluid where we construct the intermolecular effective potential and evaluate the CG molecular model. Our algorithm for calculating the free energy involves an improved Wang-Landau (WL) algorithm, which not only works more efficiently than the standard WL algorithm, but also can work in high-dimensional spaces.
Zhou
Xin
X
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA. xzhou@lanl.gov
Jiang
Yi
Y
Rasmussen
Steen
S
Ziock
Hans
H
D000465:Algorithms; D008958:Models, Molecular; D008968:Molecular Conformation; D009010:Monte Carlo Method; D013816:Thermodynamics