Molecular Dynamics with Very Large Time Steps for the Calculation of Solvation Free Energies

Journal of Chemical Theory and Computation
Charlles R A Abreu, Mark E Tuckerman

Abstract

In multiple time scale molecular dynamics, the use of isokinetic constraints along with massive thermostatting has enabled the adoption of very large integration steps, well beyond the limits imposed by resonance artifacts in standard algorithms. In this work, we present two new contributions to this topic. First, we investigate the velocity distribution and the temperature-kinetic energy relationship associated with the isokinetic Nosé-Hoover family of methods, showing how they depend on the number of thermostats attached to each atomic degree of freedom. Second, we investigate the performance of these methods in the calculation of solvation free energies, the determination of which is often key for understanding the partition of a chemical species among distinct environments. We show how one can extract this property from canonical (constant-NVT) simulations and compare the result to experimental data obtained at a specific pressure. Finally, we demonstrate that large time steps can, in fact, be used to improve the efficiency of these calculations and that attaching multiple thermostats per degree of freedom is beneficial for effectively exploring the configurational space of a molecular system.

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Oct 24, 2002·Journal of Computational Chemistry·Araz JakalianChristopher I Bayly
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Jan 21, 2006·The Journal of Chemical Physics·Yujie WuGregory A Voth
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Sep 1, 2006·The Journal of Chemical Physics·Jerry B AbramsMark E Tuckerman
May 16, 2007·Physical Review Letters·Jörg Behler, Michele Parrinello
Dec 3, 2008·The Journal of Chemical Physics·Michael R Shirts, John D Chodera
May 21, 2010·Physical Review Letters·Albert P BartókGábor Csányi
Feb 26, 2011·Current Opinion in Structural Biology·John D ChoderaVijay S Pande
Jul 27, 2011·The Journal of Chemical Physics·Tri T Pham, Michael R Shirts
Sep 29, 2011·Journal of Computational Chemistry·Floris P Buelens, Helmut Grubmüller
Dec 27, 2012·The Journal of Chemical Physics·David L Mobley, Pavel V Klimovich
May 10, 2013·The Journal of Chemical Physics·Benedict Leimkuhler, Charles Matthews
Sep 1, 2011·The Journal of Physical Chemistry Letters·Pan WuWeitao Yang
Jun 15, 2014·Journal of Computer-aided Molecular Design·David L Mobley, J Peter Guthrie
Jul 1, 2014·Journal of Computer-aided Molecular Design·Sreeja Parameswaran, David L Mobley
Mar 11, 2014·Journal of Chemical Theory and Computation·Levi N NadenMichael R Shirts
Jul 10, 2012·Journal of Chemical Theory and Computation·Vytautas GapsysBert L de Groot
Jun 8, 2010·Journal of Chemical Theory and Computation·Joseph A MorroneB J Berne
Jul 13, 2010·Journal of Chemical Theory and Computation·Michael P EastwoodDavid E Shaw
Jan 1, 2007·Journal of Chemical Theory and Computation·John D ChoderaKen A Dill
Apr 8, 2016·Journal of Chemical Theory and Computation·Daniel T Margul, Mark E Tuckerman
Apr 13, 2017·Annual Review of Biophysics·David L Mobley, Michael K Gilson
Jun 11, 2017·Journal of Computational Chemistry·Matthew HargerPengyu Ren
Jul 6, 2017·Accounts of Chemical Research·Robert AbelRichard A Friesner
Jul 27, 2017·PLoS Computational Biology·Peter EastmanVijay S Pande
Oct 24, 2017·Journal of Chemical and Engineering Data·Guilherme Duarte Ramos MatosDavid L Mobley
Nov 8, 2017·Journal of Chemical Theory and Computation·Brian K RadakBenoît Roux
Dec 16, 2017·Journal of Chemical Information and Modeling·Zoe CourniaWoody Sherman
Jan 15, 2018·The Journal of Chemical Physics·Pei-Yang Chen, Mark E Tuckerman
Sep 4, 2018·Journal of Chemical Theory and Computation·Joshua A RackersJay W Ponder
Sep 7, 2018·PloS One·Pascal T Merz, Michael R Shirts
Nov 12, 2018·Journal of Computer-aided Molecular Design·Andrea RizziJohn D Chodera
Mar 5, 2019·Journal of Chemical Theory and Computation·Alex AlbaughTeresa Head-Gordon
Mar 25, 2019·The Journal of Chemical Physics·Ana J Silveira, Charlles R A Abreu
Apr 3, 2019·Journal of Chemical Theory and Computation·Guilherme Duarte Ramos MatosDavid L Mobley

❮ 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.