Velocity jump processes: An alternative to multi-timestep methods for faster and accurate molecular dynamics simulations

The Journal of Chemical Physics
Pierre MonmarchéJean-Philip Piquemal

Abstract

We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time step specific to each atom-atom pair (two-body) interactions. We start by introducing the formalism of the new velocity jump molecular dynamics, ergodic with respect to the canonical measure. We then introduce the new BOUNCE integrator that allows for long-range forces to be evaluated at random and optimal time steps, leading to strong savings in direct space. The accuracy and computational performances of a first BOUNCE implementation dedicated to classical (non-polarizable) force fields are tested in the cases of pure direct-space droplet-like simulations and of periodic boundary conditions (PBC) simulations using Smooth Particle Mesh Ewald method. An analysis of the capability of BOUNCE to reproduce several condensed-phase properties is provided. Since electrostatics and van der Waals two-body contributions are evaluated much less often than with standard integrators using a 1 fs time step, up to a 400% direct-space acceleration is observed. Applying the reversible reference system propagator algorithms [RESPA(1)] to reciprocal-space (many-body) interactions allows BOUNCE-RESPA(1) to maintain large...Continue Reading

References

Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Jan 12, 2011·The Journal of Chemical Physics·Joseph A MorroneB J Berne
Apr 3, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·E A J F Peters, G de With
May 10, 2013·The Journal of Chemical Physics·Benedict Leimkuhler, Charles Matthews
Dec 5, 2013·Journal of Computational Chemistry·Antti-Pekka Hynninen, Michael F Crowley
Jun 8, 2010·Journal of Chemical Theory and Computation·Joseph A MorroneB J Berne
Apr 8, 2016·Journal of Chemical Theory and Computation·Daniel T Margul, Mark E Tuckerman
Nov 8, 2016·Nature Methods·Jing HuangAlexander D MacKerell
Mar 5, 2019·Journal of Chemical Theory and Computation·Alex AlbaughTeresa Head-Gordon
Mar 28, 2019·Annual Review of Biophysics·Zhifeng JingPengyu Ren
May 6, 2019·The Journal of Physical Chemistry Letters·Louis LagardèreJean-Philip Piquemal
Dec 24, 2019·Frontiers in Molecular Biosciences·Josef Melcr, Jean-Philip Piquemal

❮ Previous
Next ❯

Citations

Mar 17, 2021·The Journal of Chemical Physics·Charles L BrooksEmad Tajkhorshid
May 8, 2021·Accounts of Chemical Research·Daniele LocoJean-Philip Piquemal

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Behavioral Healthcare
Debra Neal
Journal of Thoracic Imaging
Christopher M WalkerGautham P Reddy
Journal of Applied Physiology
Giovanni A Cavagna
© 2021 Meta ULC. All rights reserved