Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics – Monte Carlo Canonical Propagation Algorithm

Type: Article

Publication Date: 2016-02-26

Citations: 17

DOI: https://doi.org/10.1021/acs.jctc.5b00706

Abstract

A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method.

Locations

  • Journal of Chemical Theory and Computation - View
  • PubMed Central - View
  • Europe PMC (PubMed Central) - View - PDF
  • PubMed - View

Similar Works

Action Title Year Authors
+ PDF Chat Multi-stage splitting integrators for sampling with modified Hamiltonian Monte Carlo methods 2018 Tijana Radivojević
Mario Fernández-Pendás
J. M. Sanz‐Serna
Elena Akhmatskaya
+ PDF Chat Adaptive multi-stage integration schemes for Hamiltonian Monte Carlo 2024 Lorenzo Nagar
Mario Fernández-Pendás
J. M. Sanz‐Serna
Elena Akhmatskaya
+ Adaptive multi-stage integration schemes for Hamiltonian Monte Carlo 2023 Lorenzo Nagar
Mario Fernández-Pendás
J. M. Sanz‐Serna
Elena Akhmatskaya
+ PDF Chat Adaptive Multi-Stage Integration Schemes for Hamiltonian Monte Carlo 2023 Lorenzo Nagar
Mario Fernández-Pendás
J. M. Sanz‐Serna
Elena Akhmatskaya
+ PDF Chat Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation 2017 Elena Akhmatskaya
Mario Fernández-Pendás
Tijana Radivojević
J. M. Sanz‐Serna
+ Coupling Molecular Dynamics and Direct Simulation Monte Carlo using a general and high-performance code coupling library 2020 Stephen Longshaw
Rohit Pillai
Livio Gibelli
David R. Emerson
Duncan A. Lockerby
+ Improving the Scaling and Performance of Multiple Time Stepping based Molecular Dynamics with Hybrid Density Functionals 2021 Sagarmoy Mandal
Ritama Kar
Tobias Kloeffel
Bernd Meyer
Nisanth N. Nair
+ Force-Gradient Nested Multirate Methods for Hamiltonian System 2013 Д. Н. Щербаков
Matthias Ehrhardt
Michael Günther
Mike Peardon
+ Force-Gradient Nested Multirate Methods for Hamiltonian System 2013 Dmitry Shcherbakov
Matthias J. Ehrhardt
Michael Günther
Mike Peardon
+ PDF Chat Improving the scaling and performance of multiple time stepping‐based molecular dynamics with hybrid density functionals 2022 Sagarmoy Mandal
Ritama Kar
Tobias Klöffel
Bernd Meyer
Nisanth N. Nair
+ Improving the Scaling and Performance of Multiple Time Stepping based Molecular Dynamics with Hybrid Density Functionals. 2021 Sagarmoy Mandal
Ritama Kar
Tobias Kloeffel
Bernd Meyer
Nisanth N. Nair
+ Error and timing analysis of multiple time-step integration methods for molecular dynamics 2006 Guowen Han
Yuefan Deng
James Glimm
Glenn Martyna
+ Connecting the Dots: Towards Continuous Time Hamiltonian Monte Carlo 2020 Tore Selland Kleppe
+ DMS: A Package for Multiscale Molecular Dynamics 2013 Endre Somogyi
Andrew Abi Mansour
P. Ortoleva
+ PDF Chat Handbook of Markov Chain Monte Carlo 2011 Steve Brooks
Andrew Gelman
Galin L. Jones
Xiao‐Li Meng
+ PDF Chat Lecture Notes: many-body quantum dynamics with MCTDH-X 2024 Paolo Molignini
Sunayana Dutta
Elke Faßhauer
+ Connecting the Dots: Numerical Randomized Hamiltonian Monte Carlo with State-Dependent Event Rates 2022 Tore Selland Kleppe
+ PDF Chat Combining stochastic and deterministic approaches within high efficiency molecular simulations 2013 Bruno Escribano
Elena Akhmatskaya
Jon I. Mujika
+ An Investigation on New Numerical Methods for Molecular Dynamics Simulation 2007 Nick Schafer
Radu Serban
Dan Negruţ
+ Connecting the Dots: Numerical Randomized Hamiltonian Monte Carlo with State-Dependent Event Rates 2020 Tore Selland Kleppe

Works That Cite This (0)

Action Title Year Authors