Generating Generalized Distributions from Dynamical Simulation

TL;DR

This paper introduces a flexible molecular dynamics simulation method using Nose' thermostats to efficiently sample a wide range of phase space distributions, including generalized variable temperature distributions.

Contribution

It develops numerical schemes based on Nose'-Hoover and Nose'-Poincare' thermostats for specific classes of distributions, enhancing sampling capabilities.

Findings

Formulated methods for distributions dependent on Hamiltonian and independent position-momentum distributions.

Proposed a generalized variable temperature distribution to accelerate molecular sampling.

Demonstrated the applicability of the schemes in molecular dynamics simulations.

Abstract

We present a general molecular-dynamics simulation scheme, based on the Nose' thermostat, for sampling according to arbitrary phase space distributions. We formulate numerical methods based on both Nose'-Hoover and Nose'-Poincare' thermostats for two specific classes of distributions; namely, those that are functions of the system Hamiltonian and those for which position and momentum are statistically independent. As an example, we propose a generalized variable temperature distribution that designed to accelerate sampling in molecular systems.