Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations

The Journal of Physical Chemistry Letters
Max LinkeGerhard Hummer

Abstract

We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer from significant finite-size effects. We remove the box-size dependence of the rotational diffusion coefficients by adding a hydrodynamic correction kB T/6 ηV with kB Boltzmann's constant, T the absolute temperature, η the solvent shear viscosity, and V the box volume. We show that this correction accounts for the finite-size dependence of the rotational diffusion coefficients of horse-heart myoglobin and a B-DNA dodecamer in aqueous solution. The resulting hydrodynamic radii are in excellent agreement with experiment.

References

Nov 25, 1997·Biophysical Journal·D WangT Jue
Oct 4, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M Fushiki
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Sep 25, 2007·The Journal of Physical Chemistry. B·Kazuhiro Takemura, Akio Kitao
Dec 7, 2007·The Journal of Physical Chemistry. B·Vance Wong, David A Case
Jul 3, 2008·The Journal of Physical Chemistry. B·In Suk Joung, Thomas E Cheatham
Jun 12, 2009·The Journal of Physical Chemistry. B·Robert B Best, Gerhard Hummer
Apr 22, 2010·Proteins·Kresten Lindorff-LarsenDavid E Shaw
Sep 20, 2011·Physical Chemistry Chemical Physics : PCCP·Carlos Vega, Jose L F Abascal
May 17, 2012·The Journal of Physical Chemistry. B·Kazuhiro Takemura, Akio Kitao
Nov 17, 2015·Nature Methods·Ivan IvaniModesto Orozco
Jul 8, 2016·The Journal of Physical Chemistry. B·Martin Vögele, Gerhard Hummer
Dec 15, 2016·The Journal of Physical Chemistry. B·Richard M VenableRichard W Pastor
Feb 1, 2018·The Journal of Physical Chemistry. B·Max LinkeGerhard Hummer

❮ Previous
Next ❯

Citations

Sep 19, 2018·Physical Chemistry Chemical Physics : PCCP·Falk HoffmannFrans A A Mulder
May 1, 2019·Proceedings of the National Academy of Sciences of the United States of America·Sören von BülowGerhard Hummer
Dec 19, 2018·Physical Chemistry Chemical Physics : PCCP·Grzegorz NawrockiMichael Feig
Dec 21, 2019·ACS Omega·Zahedeh BashardaneshDavid van der Spoel
Mar 17, 2021·The Journal of Chemical Physics·Yawei Liu, Asaph Widmer-Cooper
Apr 6, 2021·Journal of Chemical Theory and Computation·Zeke A Piskulich, Ward H Thompson
Dec 1, 2020·ACS Omega·Jan M Antosiewicz, Maciej Długosz
Apr 21, 2021·Journal of Chemical Theory and Computation·Elizabeth A PloetzPaul E Smith
Jul 27, 2021·Journal of Biomolecular Structure & Dynamics·Gouri S JasKrzysztof Kuczera
Jul 17, 2021·Biophysical Journal·Natalia OstrowskaJoanna Trylska
May 24, 2019·The Journal of Physical Chemistry. B·Navaneeth HaridasanSarith P Sathian
Nov 26, 2020·The Journal of Physical Chemistry Letters·Calen J LeverantTodd M Alam

❮ 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

The Journal of Chemical Physics
Thomas F Miller, David E Manolopoulos
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme
S Neya, N Funasaki
Physical Review. B, Condensed Matter
J K Freericks, L M Falicov
Journal of Chemical Theory and Computation
Pauline SimonninBenjamin Rotenberg
© 2022 Meta ULC. All rights reserved