Coarse-grained molecular dynamics: Nonlinear finite elements and finite temperature

Coarse Grained Molecular Dynamics and the Atomic Limit of Finite Elements

We develop a novel technique for simulation of the mechanics of micron scale solid systems Coarse Grained Molecular Dynamics CGMD It captures the important atomistic e ects without the computational cost of conventional molecular dynamics MD The CGMD equations of motion are derived directly from nite temperature MD through a statistical coarse graining procedure so they agree with MD as the mes...

Coarse Grained Molecular Dynamics

Coarse-grained protein molecular dynamics simulations.

A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse grain...

Coarse-grained molecular dynamics simulations of biomolecules

Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances...

Probability Distribution Function of the Coarse-grained Scalar Field at Finite Temperature

We present a formalism to calculate the probability distribution function of a scalar field coarse-grained over some spatial scales with a Gaussian filter at finite temperature. As an application, we investigate the role of subcritical fluctuations in the electroweak phase transition in the minimal standard model. It is concluded that the universe was in a mixed state of true and false vacua al...