Highlight Seminar

TYC Soiree

Jean-Philip Piquemal - Sorbonne University, Paris

Thursday 17th October 2019
Time: 5pm
Venue: G.O. Jones Building - Room 6.10, Mile End Campus, Queen Mary University of London
Contact: Alston Misquitta

Scalable polarizable molecular dynamics using Tinker-HP


Jean-Philip Piquemal1,2,3


1. Sorbonne Université, Paris, France.
2. Institut Universitaire de France, 75005, Paris, France.
3. Department of Biomedical Engineering, the University of Texas at Austin, TX, USA.

Abstract:
Tinker-HP is a CPU based, double precision, massively parallel package dedicated to long polarizable molecular dynamics simulations and to polarizable QM/MM. Tinker-HP is an evolution of the popular Tinker package (http://tinker-hp.ip2ct.upmc.fr/) that conserves it simplicity of use but brings new capabilities allowing performing very long molecular dynamics simulations on modern supercomputers that use thousands of cores. Indeed, this project gathers scientists from various fields including Chemistry, Applied Mathematics and Biomolecular Engineering and redefined completely the algorithmic of usual polarizable simulations package.

The Tinker-HP approach offers various strategies using domain decomposition techniques for periodic boundary conditions in the framework of the (N)log(N) Smooth Particle Mesh Ewald or using polarizable continuum simulations through the new generation ddCosmo approach. Tinker-HP proposes a high performance scalable computing environment for polarizable force fields giving access to large systems up to millions of atoms. I will present the performances and scalability of the software in the context of the AMOEBA force field and show the incoming new features including the advanced SIBFA polarizable molecular mechanics approach and the density based GEM force field as well as newly available "fully polarizable" QM/MM capabilities.

Various benchmarks and examples on biomolecular systems will be provided on several architectures showing that the approach is competitive with GPUs for small and medium size systems but allows addressing larger molecules on modern supercomputers. As the present implementation is clearly devoted to petascale applications, the applicability of such an approach to future exascale machines will be exposed and future directions of Tinker-HP discussed including the new GPUs-based implementation.

References
1) Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of
Large Complex Systems with Advanced Polarizable Force Fields. L. Lagardère, L.-H. Jolly, F.
Lipparini, F. Aviat, B. Stamm, Z. F. Jing, M. Harger, H. Torabifard, G. A. Cisneros, M. J.
Schnieders, N. Gresh, Y. Maday, P. Ren, J. W. Ponder, J.-P. Piquemal, Chem. Sci., 2018, 9, 956-
972 (Open Access)

2) Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point
Dipole Polarizable Embeddings. D. Loco, L. Lagardère, G. A. Cisneros, G. Scalmani, M. Frisch,
F. Lipparini, B. Mennucci, J.-P. Piquemal, Chem. Sci., 2019, 10, 7200-7211 (Open Access)

3) Raising the Performance of the Tinker-HP Molecular Modeling Package [Article v1.0]. L. H.
Jolly, A. Duran, L. Lagardère, J. W. Ponder, P. Y. Ren, J.-P. Piquemal, LiveCoMS, 2019, en ligne
(Open Access) DOI: 10.33011/livecoms.1.2.10409

Biography

Jean-Philip Piquemal has been trained as a Quantum Chemist at Université Pierre et Marie Curie (UPMC, Paris). After his PhD (2004) and a 2-year postdoctorate as an NIH fellow at the National Institute of Environmental Health Sciences (NIEHS, USA), he became Assistant Professor at UPMC in 2006. He defended his Research Habilitation (HDR) in 2009 to become Full Professor in 2011. In 2016 he was nominated as Junior Member of the Institut Universitaire de France (Research Chair 2016-2021). He is currently Distinguished Professor (Exceptional Class, PRCE1) in Theoretical Chemistry at Sorbonne Université (SU) and Director of the Laboratoire de Chimie Théorique (LCT, UMR 7616 SU/CNRS). He is PI of the ERC EMC2 initiative (2019-2025).

His research is devoted to theoretical chemistry and includes methodological/software developments in multiscale quantum chemistry for large systems, new generation polarizable force fields and quantum chemical topology. This work is performed in strong interdisciplinary interactions with Applied Mathematics and High-Performance Computing.

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