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Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
Author(s) -
Huang Jing,
Lemkul Justin A.,
Eastman Peter K.,
MacKerell Alexander D.
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25339
Subject(s) - force field (fiction) , molecular dynamics , polarizability , field (mathematics) , computer science , computational science , drude model , statistical physics , computational chemistry , physics , chemistry , molecule , quantum mechanics , mathematics , artificial intelligence , pure mathematics
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.