Literature DB >> 26146490

OpenMM: A Hardware Independent Framework for Molecular Simulations.

Peter Eastman1, Vijay S Pande2.   

Abstract

The wide diversity of computer architectures today requires a new approach to software development. OpenMM is a framework for molecular mechanics simulations, allowing a single program to run efficiently on a variety of hardware platforms.

Entities:  

Keywords:  Abstraction Layer; Graphics Processing Unit; Molecular Simulation

Year:  2015        PMID： 26146490      PMCID： PMC4486654          DOI： 10.1109/MCSE.2010.27

Source DB:  PubMed          Journal:  Comput Sci Eng        ISSN： 1521-9615            Impact factor:   2.080


  3 in total

1.  Accelerating molecular modeling applications with graphics processors.

Authors:  John E Stone; James C Phillips; Peter L Freddolino; David J Hardy; Leonardo G Trabuco; Klaus Schulten
Journal:  J Comput Chem       Date:  2007-12       Impact factor: 3.376

2.  Accelerating molecular dynamic simulation on graphics processing units.

Authors:  Mark S Friedrichs; Peter Eastman; Vishal Vaidyanathan; Mike Houston; Scott Legrand; Adam L Beberg; Daniel L Ensign; Christopher M Bruns; Vijay S Pande
Journal:  J Comput Chem       Date:  2009-04-30       Impact factor: 3.376

3.  Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.

Authors:  Peter Eastman; Vijay S Pande
Journal:  J Comput Chem       Date:  2010-04-30       Impact factor: 3.376
  3 in total
  60 in total

1.  Simbios: an NIH national center for physics-based simulation of biological structures.

Authors:  Scott L Delp; Joy P Ku; Vijay S Pande; Michael A Sherman; Russ B Altman
Journal:  J Am Med Inform Assoc       Date:  2011-11-10       Impact factor: 4.497

2.  Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Authors:  Jerome P Nilmeier; Gavin E Crooks; David D L Minh; John D Chodera
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

3.  Neurotoxins from snake venoms and α-conotoxin ImI inhibit functionally active ionotropic γ-aminobutyric acid (GABA) receptors.

Authors:  Denis S Kudryavtsev; Irina V Shelukhina; Lina V Son; Lucy O Ojomoko; Elena V Kryukova; Ekaterina N Lyukmanova; Maxim N Zhmak; Dmitry A Dolgikh; Igor A Ivanov; Igor E Kasheverov; Vladislav G Starkov; Joachim Ramerstorfer; Werner Sieghart; Victor I Tsetlin; Yuri N Utkin
Journal:  J Biol Chem       Date:  2015-07-28       Impact factor: 5.157

Review 4.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

5.  Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.

Authors:  John D Chodera; William C Swope; Frank Noé; Jan-Hendrik Prinz; Michael R Shirts; Vijay S Pande
Journal:  J Chem Phys       Date:  2011-06-28       Impact factor: 3.488

6.  The Hsp70 interdomain linker is a dynamic switch that enables allosteric communication between two structured domains.

Authors:  Charles A English; Woody Sherman; Wenli Meng; Lila M Gierasch
Journal:  J Biol Chem       Date:  2017-07-28       Impact factor: 5.157

7.  Long Timestep Molecular Dynamics on the Graphical Processing Unit.

Authors:  James C Sweet; Ronald J Nowling; Trevor Cickovski; Christopher R Sweet; Vijay S Pande; Jesús A Izaguirre
Journal:  J Chem Theory Comput       Date:  2013-08-13       Impact factor: 6.006

8.  Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations.

Authors:  Bing Xie; Trung Hai Nguyen; David D L Minh
Journal:  J Chem Theory Comput       Date:  2017-05-01       Impact factor: 6.006

9.  United polarizable multipole water model for molecular mechanics simulation.

Authors:  Rui Qi; Lee-Ping Wang; Qiantao Wang; Vijay S Pande; Pengyu Ren
Journal:  J Chem Phys       Date:  2015-07-07       Impact factor: 3.488

10.  Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3.

Authors:  Radim Osicka; Adriana Osickova; Shakir Hasan; Ladislav Bumba; Jiri Cerny; Peter Sebo
Journal:  Elife       Date:  2015-12-09       Impact factor: 8.140
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