GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Journal of Chemical Theory and Computation
Berk HessErik Lindahl


Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.


Sep 1, 1995·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·B L HolianR Ravelo
Apr 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Young Min RheeVijay S Pande
Jul 9, 2005·Science·Stephen B LongRoderick Mackinnon
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
May 20, 2006·The Journal of Chemical Physics·Kevin J BowersDavid E Shaw
Feb 9, 2007·The Journal of Chemical Physics·Ross A LippertDavid E Shaw
Apr 4, 2007·Journal of Computational Chemistry·Carsten KutznerHelmut Grubmüller
Apr 7, 2007·The Journal of Chemical Physics·Simone MeloniLuciano Colombo
Jan 1, 2008·Journal of Chemical Theory and Computation·Berk Hess

❮ Previous
Next ❯


Jan 16, 2019·PLoS Computational Biology·Dheeraj DubeSurajit Sengupta
Jan 18, 2018·Journal of Computer-aided Molecular Design·Stefano Della Longa, Alessandro Arcovito
Jan 16, 2019·Soft Matter·Federico Elías-WolffErik G Brandt
Sep 11, 2018·Journal of Biomolecular Structure & Dynamics·Paulo Sérgio Alves BuenoFlávio Augusto Vicente Seixas
Jan 24, 2019·Interdisciplinary Sciences, Computational Life Sciences·Dino Franklin
Oct 26, 2018·Journal of the American Society for Mass Spectrometry·O Tara LiyanageElyssia S Gallagher
Sep 28, 2018·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Jian ZhanYaoqi Zhou
Jan 31, 2019·Journal of Computational Chemistry·Arghya ChakravortyEmil Alexov
Jan 20, 2019·The FEBS Journal·Luisa CastagnoliElena Santonico
Feb 13, 2018·Nature Communications·Takashi NakaokuKoichi Goto
Jan 27, 2019·Angewandte Chemie·Francesco ColizziModesto Orozco
Oct 31, 2008·Physical Chemistry Chemical Physics : PCCP·David van der SpoelCarl Caleman
Mar 13, 2009·Physical Chemistry Chemical Physics : PCCP·Alessandra VillaChristine Peter
Feb 5, 2009·Journal of Computational Chemistry·Mark S FriedrichsVijay S Pande
Feb 21, 2018·Nature Communications·Chaowei ShiHan Sun
Feb 22, 2018·Journal of Molecular Modeling·Evanildo G LacerdaSylvio Canuto
Jul 3, 2009·Nature·Alexander SteinReinhard Jahn
Feb 25, 2018·Journal of Molecular Modeling·Abbas YousefpourSepideh Amjad-Iranagh
Oct 23, 2009·Chembiochem : a European Journal of Chemical Biology·Ricardo J F BrancoJürgen Pleiss
Feb 11, 2010·Physical Chemistry Chemical Physics : PCCP·Ivana BesseováJirí Sponer
Oct 23, 2009·Journal of Computational Chemistry·Peter Eastman, Vijay S Pande
Nov 6, 2009·Physical Chemistry Chemical Physics : PCCP·Matteus LindgrenPer-Olof Westlund
Dec 1, 2009·Nanotechnology·Sony JosephPredrag S Krstic
Dec 25, 2009·Journal of Computational Chemistry·Elad ProjectMenachem Gutman
Dec 23, 2009·Journal of Computational Chemistry·Bogdan LevSergei Yu Noskov
Jan 21, 2010·Journal of Computational Chemistry·Andrzej J RzepielaSiewert J Marrink
Mar 26, 2010·Journal of Computational Chemistry·Maarten G WolfGerrit Groenhof
Apr 10, 2010·Physical Chemistry Chemical Physics : PCCP·Vincenzo BaroneGiacomo Prampolini
Oct 12, 2010·Journal of Computational Chemistry·Bernhard KnappWolfgang Schreiner
May 22, 2010·Physical Chemistry Chemical Physics : PCCP·Marina RadoulDaniella Goldfarb

❮ Previous
Next ❯

Related Concepts

Trending Feeds


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 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.


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.