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OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics [article]

Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks (+1 others)
2016 bioRxiv   pre-print
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility.  ...  This makes it an ideal tool for researchers developing new simulation methods, and also allows those new methods to be immediately available to the larger community.  ...  Availability and Future Directions OpenMM is available from http://openmm.org. Ongoing development is conducted through the Github community at https://github.com/pandegroup/openmm.  ... 
doi:10.1101/091801 fatcat:i5o5tjnvpzcflf365v3f5qdbsm

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Peter Eastman, Jason Swails, John D. Chodera, Robert T. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks (+2 others)
2017 PLoS Computational Biology  
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility.  ...  A complete molecular dynamics package is, of course, much more than just a simulation engine.  ...  Development of OpenMM was supported by Simbios via the NIH Roadmap for Medical Research Grant U54 GM072970, and by NIH grant R01-GM062868. The authors thank Daniel L.  ... 
doi:10.1371/journal.pcbi.1005659 pmid:28746339 pmcid:PMC5549999 fatcat:f2uellukczerhjfcjn4ldniki4

OpenMM: A Hardware-Independent Framework for Molecular Simulations

Peter Eastman, Vijay Pande
2010 Computing in science & engineering (Print)  
OpenMM is a framework for molecular mechanics simulations, allowing a single program to run efficiently on a variety of hardware platforms.  ...  The wide diversity of computer architectures today requires a new approach to software development.  ...  Acknowledgements The development of OpenMM was supported by Simbios via the NIH Roadmap for Medical Research Grant U54 GM072970. It is available at http://simtk.org/home/openmm.  ... 
doi:10.1109/mcse.2010.27 pmid:26146490 pmcid:PMC4486654 fatcat:4jtjna7xkrg5bd3x2uqkbhq3a4

D1.5: ClassicalMD E-CAMModules IV

David Swenson
2020 Zenodo  
OpenPath-Sampling wraps around other dynamics engines, such as OpenMM, and leverages the performance that is already developed in those. n2p2 is a software package supporting parallelization via Message  ...  In this report for Deliverable 1.5 of E-CAM, 9 software modules in classical dynamics are presented. These modules represent improvements and new features in response to the needs of users.  ...  Introduction Notwithstanding the exponential increase in computing power over the last few decades and the development of efficient molecular dynamics algorithms, many processes are still beyond the reach  ... 
doi:10.5281/zenodo.3699553 fatcat:kxxb773zinhjrjypqevkclbpky

E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands

Michael Kilgour, Tao Liu, Ilya S. Dementyev, Lena Simine
2022 Journal of Open Source Software  
The operation of this supercomputer is funded by the Canada Foundation for Innovation (CFI).  ...  Acknowledgements Funding from the NSERC Discovery grant RGPIN-201924734 and an NSERC PDF for M.K. is greatly appreciated.  ...  The MMB outputs, as initial structures, are then passed to MD simulation for relaxation. The third module, OpenMM (Eastman et al., 2017) , is the molecular dynamics engine powering E2EDNA 2.0.  ... 
doi:10.21105/joss.04182 fatcat:m26mgf4kgvhdtjooxkeyqzhd24

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors

David R. Glowacki, Michael O'Connor, Gaetano Calabró, James Price, Philip Tew, Thomas Mitchell, Joseph Hyde, David P. Tew, David J. Coughtrie, Simon McIntosh-Smith
2014 Faraday discussions  
In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors.  ...  field of interactive molecular dynamics seems destined to expand.  ...  of England, and Arts Council England.  ... 
doi:10.1039/c4fd00008k pmid:25340458 fatcat:hfkjis2pdfdthli6255cktpewm

Tinker 8: Software Tools for Molecular Design

Joshua A. Rackers, Zhi Wang, Chao Lu, Marie L. Laury, Louis Lagardère, Michael J. Schnieders, Jean-Philip Piquemal, Pengyu Ren, Jay W. Ponder
2018 Journal of Chemical Theory and Computation  
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions  ...  In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical  ...  Acknowledgements JWP and PR wish to thank the National Institutes of Health NIGMS for support of recent force field and software development via awards R01 GM106137 and R01 GM114237.  ... 
doi:10.1021/acs.jctc.8b00529 pmid:30176213 pmcid:PMC6335969 fatcat:dr6m2xthnzaexhiubijfe4wjme

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

Evan J. Arthur, Charles L. Brooks
2016 Journal of Computational Chemistry  
We find that much of the algorithm scales linearly with an increase of system size, which makes this water model cost effective for solvating large systems.  ...  Two fundamental challenges of simulating biologically relevant systems are the rapid calculation of the energy of solvation, and the trajectory length of a given simulation.  ...  Josh Buckner for their assistance in CHARMM and OpenMM programming advice. This work was funded by the National Institutes of Health through grant GM103695 to CLB. Bibliography  ... 
doi:10.1002/jcc.24280 pmid:26786647 pmcid:PMC4801733 fatcat:ngj3p632kbgzzbynoxnvgrddvm

SMOG 2 and OpenSMOG: Extending the limits of structure-based models [article]

Antonio B. de Oliveira, Vinícius G. Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, Esteban Dodero-Rojas, Udayan Mohanty, Jeffrey K. Noel, Jose N. Onuchic, Paul C. Whitford
2021 bioRxiv   pre-print
AbstractApplying simulations with structure-based (Gō-like) models has proven to be an effective strategy for investigating the factors that control biomolecular dynamics.  ...  To facilitate the development and application of this broad class of models, we previously released the SMOG 2 software package.  ...  SMOG 1 provided a web-based interface for generating structure-based models that could be simulated with Gromacs, 20,21 a high-performance molecular dynamics package.  ... 
doi:10.1101/2021.08.15.456423 fatcat:vkz4k7vvn5g2lnmrx2ugadjwp4

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

Peter Eastman, Vijay S. Pande
2010 Journal of Chemical Theory and Computation  
We introduce a new algorithm, the Constant Constraint Matrix Approximation (CCMA), for constraining distances in molecular simulations.  ...  It combines the best features of many existing algorithms while avoiding their defects: it is fast, stable, can be applied to arbitrary constraint topologies, and can be efficiently implemented on modern  ...  Acknowledgments The authors would like to thank Michael Sherman for useful conversations related to the design of this algorithm.  ... 
doi:10.1021/ct900463w pmid:20563234 pmcid:PMC2885791 fatcat:yp3tiqcahnh4dgntfrfrxndv7i

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

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
2015 Biophysical Journal  
As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis  ...  We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats.  ...  This environment is ideal for both rapid development and high performance, as computational kernels can be implemented in the languages C, Cþþ, and FORTRAN, but made available within a more user-friendly  ... 
doi:10.1016/j.bpj.2015.08.015 pmid:26488642 pmcid:PMC4623899 fatcat:dxvukd7e4zhknirknrrz3lxt3i

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations [article]

Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson (+5 others)
2019 biorxiv/medrxiv   pre-print
To rank the methods, we developed an efficiency statistic based on bias and variance of the free energy estimates.  ...  weighted ensemble of trajectories) methodologies implemented with the GROMACS, AMBER, NAMD, or OpenMM simulation engines.  ...  627 of the alchemical transformations. 3. 7 7 insight, we performed molecular dynamics simulations of OA-G3 at 1 atm and 100 atm 656 in NPT using the GROMACS Berendsen barostat and the OpenMM Monte Carlo  ... 
doi:10.1101/795005 fatcat:npp23xdnibat7nobiu3c5s4j6a

Polarizable Multipolar Molecular Dynamics Using Distributed Point Charges [article]

Mike Devereux, Marco Pezzella, Shampa Raghunathan, Markus Meuwly
2020 arXiv   pre-print
Comparisons of the molecular electrostatic potential (MEP), electrostatic interaction energies, and bulk properties from molecular dynamics simulations for a range of models from simple TIPnP (n = 3-5)  ...  algorithm for thermodynamic integration.  ...  ACKNOWLEDGEMENT The authors acknowledge financial support from the Swiss National Foundation for Research for their support within the NCCR MUST program and project 200021-117810.  ... 
arXiv:2008.12042v2 fatcat:omsy3tkqkjgpbimspvrzfehyky

Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking [article]

Mallory R Tollefson, Jacob Litman, Guowei Qi, Robert J Marini, Claire E O'Connell, Matthew J Wipfler, Hernan V Bernabe, William TA Tollefson, Thomas L Casavant, Terry A Braun, Richad JH Smith, Michael John Schnieders
2019 bioRxiv   pre-print
The majority of these variants are classified as 'variants of uncertain significance' to reflect our inability to ascribe a phenotypic effect to the observed amino acid change.  ...  Hearing loss is associated with ~8100 mutations in 152 genes, and within the coding regions of these genes are over 60,000 missense variants.  ...  High quality protein structural models, in turn, provide optimal starting points for downstream molecular dynamics algorithms that can be used to analyze missense variations.  ... 
doi:10.1101/556258 fatcat:skc33gnxfzbi3lxhxuy7rxmym4

WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis

Matthew C. Zwier, Joshua L. Adelman, Joseph W. Kaus, Adam J. Pratt, Kim F. Wong, Nicholas B. Rego, Ernesto Suárez, Steven Lettieri, David W. Wang, Michael Grabe, Daniel M. Zuckerman, Lillian T. Chong
2015 Journal of Chemical Theory and Computation  
The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g., GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages  ...  To enable the simulation of rare events at any scale (e.g., atomistic, cellular), we have developed an opensource, interoperable, and highly scalable software package for the execution and analysis of  ...  , and Cython enables rapid development of readable source code without a substantial sacrifice of run-time performance. 3.2.  ... 
doi:10.1021/ct5010615 pmid:26392815 pmcid:PMC4573570 fatcat:6mgeywghdjgjbh2nigaop633gq
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