English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem.Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards toaccelerate molecular dynamics simulations using polarizable many-body forcefields. The new high-performance module allows for an efficient use of single-and multi-GPU architectures ranging from research laboratories to modernsupercomputer centers. After detailing an analysis of our general scalablestrategy that relies on OpenACC and CUDA, we discuss the various capabilitiesof the package. Among them, the multi-precision possibilities of the code arediscussed. If an efficient double precision implementation is provided topreserve the possibility of fast reference computations, we show that a lowerprecision arithmetic is preferred providing a similar accuracy for moleculardynamics while exhibiting superior performances. As Tinker-HP is mainlydedicated to accelerate simulations using new generation point dipolepolarizable force field, we focus our study on the implementation of the AMOEBAmodel. Testing various NVIDIA platforms including 2080Ti, 3090, V100 and A100cards, we provide illustrative benchmarks of the code for single- andmulti-cards simulations on large biosystems encompassing up to millions ofatoms. The new code strongly reduces time to solution and offers the bestperformances to date obtained using the AMOEBA polarizable force field.Perspectives toward the strong-scaling performance of our multi-node massiveparallelization strategy, unsupervised adaptive sampling and large scaleapplicability of the Tinker-HP code in biophysics are discussed. The presentsoftware has been released in phase advance on GitHub in link with the HighPerformance Computing community COVID-19 research efforts and is free forAcademics (see https://github.com/TinkerTools/tinker-hp).

journal of chemical theory and computation

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