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Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

Matthew Harger, Daniel Li, Zhi Wang, Kevin Dalby, Louis Lagardère, Jean-Philip Piquemal, Jay Ponder, Pengyu Ren
2017 Journal of Computational Chemistry  
Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ~200-fold improvement in  ...  We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach.  ...  Therefore, the AMOEBA on GPU implementation described here(Tinker-OpenMM) constitutes the first available platform for free energy perturbation simulations on GPUs using a polarizable force field.  ... 
doi:10.1002/jcc.24853 pmid:28600826 fatcat:qrchfkdduzdatkpbg7zn6ljery

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

Louis Lagardère, Luc-Henri Jolly, Filippo Lipparini, Félix Aviat, Benjamin Stamm, Zhifeng F. Jing, Matthew Harger, Hedieh Torabifard, G. Andrés Cisneros, Michael J. Schnieders, Nohad Gresh, Yvon Maday (+3 others)
2018 Chemical Science  
Acknowledgements This work was made possible thanks to the French state funds managed by the CalSimLab LABEX and the ANR within the Investissements d'Avenir program (reference ANR-11-IDEX-0004-02) and  ...  Such studies will benet from the computational platform introduced in Tinker-OpenMM that allows computing absolute binding and relative alchemical approach as well as relative binding affinities of ligands  ...  It led to a GPU version of the code denoted Tinker-OpenMM. 34 The code is based both on Tinker and on the OpenMM library (now version 7 (ref. 35 )) which pioneered the use of GPUs with polarizable force  ... 
doi:10.1039/c7sc04531j pmid:29732110 pmcid:PMC5909332 fatcat:7gur7v4oyvhg3ok77car6sr3hq

Development and analysis of Tinker-OpenMM as a GPU-based free energy perturbation engine

Matthew Thomas Harger, Austin, The University Of Texas At, Austin, The University Of Texas At, Pengyu Ren, Kevin N. Dalby
In this dissertation, I describe the addition of GPU-based absolute and relative free energy calculation methods using polarizable force field AMOEBA to Tinker-OpenMM.  ...  I then proceed to test the capabilities of this platform by studying the binding free energy and binding structures of derivatives of the MELK inhibitor IN17.  ...  The authors are grateful for support by grants from the National Institutes of Health (R01GM106137 and R01GM114237) and from the Cancer Prevention Research Institute of Texas grant (RP160657 and RP180880  ... 
doi:10.26153/tsw/3259 fatcat:df7tpu7fgjd7dgoz442jo53wnq

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  
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  ...  The package runs on Linux, macOS, and Windows systems.  ...  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

Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems [article]

Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Thibaut Very, Isabelle Dupays, Zhi Wang, Théo Jaffrelot Inizan, Frédéric Célerse, Pengyu Ren, Jay W. Ponder, Jean-Philip Piquemal
2021 arXiv   pre-print
The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field.  ...  As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model.  ...  This project was initiated in 2019 with a "Contrat de Progrès" grant from GENCI (France) in collaboration with HPE and NVIDIA to port Tinker-HP on the Jean Zay HPE SGI 8600 GPUs system (IDRIS supercomputer  ... 
arXiv:2011.01207v4 fatcat:be7wgtzaxbasjagguniha3l3hm

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

Timothy J. Giese, Darrin M. York
2018 Journal of Chemical Theory and Computation  
We apply the PI-TI method with HREM on GPUs in AMBER to predict pK a values in double stranded RNA molecules and make comparison with experiments.  ...  The PI-TI method has the practical advantage that no modification of the MD code is required to propagate the dynamics, and unlike with linear alchemical mixing, only one electrostatic evaluation is needed  ...  GM107485 and GM62248).  ... 
doi:10.1021/acs.jctc.7b01175 pmid:29357243 pmcid:PMC5849537 fatcat:tis4kuvp3jganfrm32bw7hb45e