Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs - Archive ouverte HAL Access content directly
Journal Articles Journal of Computational Chemistry Year : 2017

Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs

Abstract

The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. 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 simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host–guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach.
Fichier principal
Vignette du fichier
HargerPaperJCC.pdf (1.39 Mo) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

hal-01571313 , version 1 (02-08-2017)

Identifiers

Cite

Matthew Harger, Daniel Li, Zhi Wang, Kevin Dalby, Louis Lagardère, et al.. Tinker-OpenMM : Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs. Journal of Computational Chemistry, 2017, 38 (23), pp.2047-2055. ⟨10.1002/jcc.24853⟩. ⟨hal-01571313⟩
336 View
543 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More