Accelerating molecular modeling applications with graphics processors

Journal of Computational Chemistry
John E StoneKlaus Schulten


Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb pot...Continue Reading


Jun 16, 1977·Nature·J A McCammonM Karplus
Sep 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·P A FitzpatrickA M Klibanov
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 1, 1997·Nature Structural Biology·I Tinoco, J S Kieft
Oct 23, 1998·Nature·A R Ferré-D'AmaréJ A Doudna
May 20, 1999·Biopolymers·V K Misra, D E Draper
Jul 10, 1999·Current Opinion in Structural Biology·S Cusack
Jun 3, 2000·Journal of Molecular Biology·V K Misra, D E Draper
Feb 17, 2001·Current Opinion in Structural Biology·S B Larson, A McPherson
Aug 23, 2001·Proceedings of the National Academy of Sciences of the United States of America·N A BakerJ A McCammon
Oct 25, 2001·Proceedings of the National Academy of Sciences of the United States of America·V K Misra, D E Draper
Mar 28, 2002·Journal of Molecular Biology·Robert W LucasAlexander McPherson
Apr 10, 2002·Journal of Computational Chemistry·Robert D SkeelDavid J Hardy
Jun 6, 2002·Journal of the American Chemical Society·In-Chul Yeh, Gerhard Hummer
Nov 8, 2002·Nature·Christopher D SnowMartin Gruebele
Sep 2, 2004·Biophysical Journal·Marcos Sotomayor, Klaus Schulten
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Oct 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Kevin Y SanbonmatsuChang-Shung Tung
Mar 15, 2006·Structure·Peter L FreddolinoKlaus Schulten
May 11, 2006·Chemical Reviews·Stewart A Adcock, J Andrew McCammon
Sep 9, 2006·Science·Maria SelmerV Ramakrishnan

❮ Previous
Next ❯


Dec 14, 2011·Journal of Computer-aided Molecular Design·Xavier Barril, F Javier Luque
Mar 27, 2013·Journal of Molecular Graphics & Modelling·M S OzhgibesovC H Cheng
Nov 16, 2011·Quarterly Reviews of Biophysics·Jeff Wereszczynski, J Andrew McCammon
Mar 12, 2010·Journal of Chemical Information and Modeling·Imran S HaqueW Patrick Walters
Mar 26, 2011·Journal of Chemical Information and Modeling·Oliver KorbThomas E Exner
Jun 24, 2011·Journal of Chemical Information and Modeling·Pu LiuEric Yang
Apr 28, 2012·Journal of Chemical Information and Modeling·Frederico PratasRicardo A Mata
Aug 29, 2013·Chemical Reviews·G Andrés CisnerosCeleste Sagui
Aug 28, 2013·Chemical Reviews·Robert O J Weinzierl
Jul 11, 2009·Chemical Reviews·Huan-Xiang Zhou, Michael K Gilson
Sep 30, 2009·Chemical Reviews·Ivet BaharIndira H Shrivastava
Feb 8, 2011·Nature Physics·Peter L FreddolinoKlaus Schulten
Jan 1, 2009·Faraday Discussions·Eduardo R Cruz-ChuKlaus Schulten
Aug 30, 2012·Journal of Biomolecular Structure & Dynamics·Hridoy R Bairagya, Bishnu P Mukhopadhyay
Apr 14, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·David DynermanJulie C Mitchell
Feb 12, 2011·Briefings in Bioinformatics·Matthieu ChaventMarc Baaden
Aug 6, 2010·Bioinformatics·David W Ritchie, Vishwesh Venkatraman
Mar 6, 2012·BMC Genomics·Narges Sharif RazavianChristopher J Langmead
Oct 18, 2011·Journal of Computational and Graphical Statistics : a Joint Publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America·Anthony LeeChristopher C Holmes
Aug 27, 2013·PloS One·Karen R KharJohn Karanicolas
Oct 16, 2012·The Journal of Chemical Physics·Panagiotis AngelikopoulosPetros Koumoutsakos
Nov 5, 2013·The Journal of Chemical Physics·Ross A LippertDavid E Shaw
Oct 23, 2013·BMC Structural Biology·Thai V HoangDavid W Ritchie
Jan 21, 2014·The Journal of Chemical Physics·Daniel TamelingAhmed E Ismail
Jun 7, 2011·The Journal of Chemical Physics·Christof SchütteEric Vanden-Eijnden
May 9, 2014·The Journal of Chemical Physics·Dario TamascelliMichele Ceotto
Jun 24, 2014·The Journal of Chemical Physics·Stan G Moore, Paul S Crozier
Mar 23, 2011·Theoretical Chemistry Accounts·Yaoqi ZhouHongxing Lei
Jul 18, 2015·International Journal of Molecular Sciences·Rongzhong LiSamuel S Cho
Feb 16, 2016·The Journal of Chemical Physics·Ron Elber
Jan 26, 2016·Journal of Chemical Theory and Computation·Edoardo Aprà, Karol Kowalski
Mar 13, 2012·Journal of Neuroscience Methods·Roy Ben-ShalomAlon Korngreen
Feb 21, 2014·Science China. Life Sciences·HuiMin LiShuQun Liu
Aug 10, 2010·Journal of Molecular Biology·Leonardo G TrabucoKlaus Schulten
Aug 3, 2010·Journal of Molecular Graphics & Modelling·John E StoneKlaus Schulten
May 11, 2010·Journal of Molecular Graphics & Modelling·Ramu AnandakrishnanAlexey V Onufriev
Feb 18, 2010·Parallel Computing·Cole Trapnell, Michael C Schatz
Feb 18, 2010·Parallel Computing·David J HardyKlaus Schulten

❮ 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.

Related Papers

Journal of Computational Chemistry
Mark S FriedrichsVijay S Pande
Journal of Molecular Graphics & Modelling
John E StoneKlaus Schulten
Journal of Computational Chemistry
James C PhillipsKlaus Schulten
© 2021 Meta ULC. All rights reserved