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

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

Content Provider	Scilit
Author	Huang, Jing Lemkul, Justin A. Eastman, Peter K. Kerell, Alexander D. Mac
Copyright Year	2018
Description	Journal: Journal of computational chemistry Presented is the implementation of the Drude force field in the open-source OpenMM simulation package allowing for access to graphical processing unit (GPU) hardware. In the Drude model, electronic degrees of freedom are represented by negatively charged particles attached to their parent atoms via harmonic springs, such that extra computational overhead comes from these additional particles and virtual sites representing lone pairs on electronegative atoms, as well as the associated thermostat and integration algorithms. This leads to an approximately fourfold increase in computational demand over additive force fields. However, by making the Drude model accessible to consumer-grade desktop GPU hardware it will be possible to perform simulations of one microsecond or more in less than a month, indicating that the barrier to employ polarizable models has largely been removed such that polarizable simulations with the classical Drude model are readily accessible and practical.
Related Links	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031474/pdf
Ending Page	1689
Page Count	8
Starting Page	1682
e-ISSN	1096987X
DOI	10.1002/jcc.25339
Journal	Journal of computational chemistry
Issue Number	21
Volume Number	39
Language	English
Publisher	Wiley-Blackwell
Publisher Date	2018-05-04
Access Restriction	Open
Subject Keyword	Journal: Journal of computational chemistry Interdisciplinary Mathematics Drude Oscillator Graphical Processing Units Molecular Dynamics Simulation Polarizable Force Field
Content Type	Text
Resource Type	Article

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