Literature DB >> 23316124

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

Peter Eastman1, Mark S Friedrichs, John D Chodera, Randall J Radmer, Christopher M Bruns, Joy P Ku, Kyle A Beauchamp, Thomas J Lane, Lee-Ping Wang, Diwakar Shukla, Tony Tye, Mike Houston, Timo Stich, Christoph Klein, Michael R Shirts, Vijay S Pande.   

Abstract

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

Entities:  

Year:  2012        PMID: 23316124      PMCID: PMC3539733          DOI: 10.1021/ct300857j

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  22 in total

1.  Quantum statistics and classical mechanics: real time correlation functions from ring polymer molecular dynamics.

Authors:  Ian R Craig; David E Manolopoulos
Journal:  J Chem Phys       Date:  2004-08-22       Impact factor: 3.488

Review 2.  Empirical force fields for biological macromolecules: overview and issues.

Authors:  Alexander D Mackerell
Journal:  J Comput Chem       Date:  2004-10       Impact factor: 3.376

3.  Efficient stochastic thermostatting of path integral molecular dynamics.

Authors:  Michele Ceriotti; Michele Parrinello; Thomas E Markland; David E Manolopoulos
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

4.  A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods.

Authors:  Himanshu Paliwal; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2011-11-14       Impact factor: 6.006

5.  Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.

Authors:  Michael R Shirts; Vijay S Pande
Journal:  J Chem Phys       Date:  2005-04-08       Impact factor: 3.488

6.  Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

Authors:  Michael R Shirts; Vijay S Pande
Journal:  J Chem Phys       Date:  2005-04-01       Impact factor: 3.488

7.  Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors:  Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal:  Proteins       Date:  2006-11-15

8.  Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

Authors:  Michael R Shirts; David L Mobley; John D Chodera; Vijay S Pande
Journal:  J Phys Chem B       Date:  2007-10-19       Impact factor: 2.991

Review 9.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

10.  Statistically optimal analysis of samples from multiple equilibrium states.

Authors:  Michael R Shirts; John D Chodera
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

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  199 in total

1.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

2.  MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

Authors:  Robert T McGibbon; Kyle A Beauchamp; Matthew P Harrigan; Christoph Klein; Jason M Swails; Carlos X Hernández; Christian R Schwantes; Lee-Ping Wang; Thomas J Lane; Vijay S Pande
Journal:  Biophys J       Date:  2015-10-20       Impact factor: 4.033

3.  Accelerating molecular simulations of proteins using Bayesian inference on weak information.

Authors:  Alberto Perez; Justin L MacCallum; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

4.  Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

Authors:  Xinqiang Ding; Jonah Z Vilseck; Ryan L Hayes; Charles L Brooks
Journal:  J Chem Theory Comput       Date:  2017-05-26       Impact factor: 6.006

5.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

6.  Molecular mechanism of GPCR-mediated arrestin activation.

Authors:  Naomi R Latorraca; Jason K Wang; Brian Bauer; Raphael J L Townshend; Scott A Hollingsworth; Julia E Olivieri; H Eric Xu; Martha E Sommer; Ron O Dror
Journal:  Nature       Date:  2018-05-02       Impact factor: 49.962

7.  Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.

Authors:  Jing Huang; Justin A Lemkul; Peter K Eastman; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-05-04       Impact factor: 3.376

8.  Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2016-10-27       Impact factor: 2.991

9.  Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP.

Authors:  Christina Schindler; Friedrich Rippmann; Daniel Kuhn
Journal:  J Comput Aided Mol Des       Date:  2017-09-12       Impact factor: 3.686

10.  Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.

Authors:  Ido Y Ben-Shalom; Zhixiong Lin; Brian K Radak; Charles Lin; Woody Sherman; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2020-11-18       Impact factor: 6.006

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