Preprint Article Version 1 This version is not peer-reviewed

High-throughput of measure-preserving integrators for constant temperature molecular dynamics simulations on GPUs

Version 1 : Received: 8 November 2018 / Approved: 9 November 2018 / Online: 9 November 2018 (15:26:49 UTC)

How to cite: Guarneros-Nolasco, L.; Terrón-Mejía, K.A.; Mulia-Rodríguez, J.; Osorio-Gonzalez, D.; López-Rendón, R.; Rodriguez-Romero, F. High-throughput of measure-preserving integrators for constant temperature molecular dynamics simulations on GPUs. Preprints 2018, 2018110250 (doi: 10.20944/preprints201811.0250.v1). Guarneros-Nolasco, L.; Terrón-Mejía, K.A.; Mulia-Rodríguez, J.; Osorio-Gonzalez, D.; López-Rendón, R.; Rodriguez-Romero, F. High-throughput of measure-preserving integrators for constant temperature molecular dynamics simulations on GPUs. Preprints 2018, 2018110250 (doi: 10.20944/preprints201811.0250.v1).

Abstract

Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological systems. However, of the excellent results that the technique has arrogated, this approach remains computationally expensive, but with the emergence of the new supercomputing technologies bases on graphics processing units graphical processing units-based systems GPUs, the perspective has changed. The GPUs allow performing large and complex simulations at a significantly reduced time. In this work, we present recent innovations in the acceleration of molecular dynamics in GPUs to simulate non-Hamiltonian systems. In particular, we show the performance of measure-preserving geometric integrator in the canonical ensemble, that is, at constant temperature. We provide a validation and performance evaluation of the code by calculating the thermodynamic properties of a Lennard-Jones fluid. Our results are in excellent agreement with reported data reported from literature, which were calculated with CPUs. The scope and limitations for performing simulations of high-throughput MD under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.

Subject Areas

High-Throughput Molecular Dynamics (HTMD) simulations; Nosé-Hoover Chain (NHC); Canonical ensemble; Graphics Processing Units (GPUs).

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