Long Timestep Molecular Dynamics on the Graphical Processing Unit.

James C Sweet, Ronald J Nowling, Trevor Cickovski, Christopher R Sweet, Vijay S Pande, Jesús A Izaguirre

Abstract read

In one paragraph

Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

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0cells of the map it votes in

8citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

Atomistic-to-Macroscopic Mechanical Modeling of (HfNbTaZr)BMaterials (Basel, Switzerland) · 2026
Article
Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories.Viruses · 2023
Review
Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.Journal of chemical information and modeling · 2023
Article
Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers.Nature communications · 2022
Article
From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021
Review
Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019
Review
Graphics processing units in bioinformatics, computational biology and systems biology.Briefings in bioinformatics · 2017
Review
Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.Biochimica et biophysica acta · 2016
Review

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

James C SweetDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Ronald J NowlingDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Trevor CickovskiDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Christopher R SweetDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Vijay S PandeDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Jesús A IzaguirreDepartment of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science, Eckerd College, Saint Petersburg, FL 33712, USA, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.

Funding

Enabling long timestep molecular dynamics on parallel CPU and GPU environmentsR01GM101935 · NIGMS · UNIVERSITY OF NOTRE DAME · PI IZAGUIRRE, JESUS ANTONIO · 2012 to 2015

$1.2M

NIGMS NIH HHS R01 GM101935

6 · The paper itself

Abstract

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 μs/day using implicit solvent models.

Identifiers

PMID24436689

DOI10.1021/ct400331r

PMCPMC3890418

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LicenceTDM

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.