Papers by Jean-Philip Piquemal
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics ... more We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms.We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed.
Status of the Gaussian Electrostatic Model, a Density-Based Polarizable Force Field
Many-Body Effects and Electrostatics in Biomolecules, 2016
A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations
Journal of chemical theory and computation, Jan 11, 2016
A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach i... more A fully polarizable implementation of the hybrid quantum mechanics/molecular mechanics approach is presented, where the classical environment is described through the AMOEBA polarizable force field. A variational formalism, offering a self-consistent relaxation of both the MM induced dipoles and the QM electronic density, is used for ground state energies and extended to electronic excitations in the framework of time-dependent density functional theory combined with a state specific response of the classical part. An application to the calculation of the solvatochromism of the pyridinium N-phenolate betaine dye used to define the solvent ET(30) scale is presented. The results show that the QM/AMOEBA model not only properly describes specific and bulk effects in the ground state but it also correctly responds to the large change in the solute electronic charge distribution upon excitation.
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields
Journal of Computational Chemistry, 2016
We introduce an initial implementation of the LICHEM software package. LICHEM can interface with ... more We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER-HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single-point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization. © 2016 Wiley Periodicals, Inc.
Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles
Journal of Computational Chemistry, 2016
We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed mul... more We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.
Addressing the Issues of Non-isotropy and Non-additivity in the Development of Quantum Chemistry-Grounded Polarizable Molecular Mechanics
Quantum Modeling of Complex Molecular Systems, 2015
ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) compute... more ABSTRACT We review two essential features of the intermolecular interaction energies (ΔE) computed in the context of quantum chemistry (QC): non-isotropy and non-additivity. Energy-decomposition analyses show the extent to which each comes into play in the separate ΔE contributions, namely electrostatic, short-range repulsion, polarization, charge-transfer and dispersion. Such contributions have their counterparts in anisotropic, polarizable molecular mechanics (APMM), and each of these should display the same features as in QC. We review examples to evaluate the performances of APMM in this respect. They bear on the complexes of one or several ligands with metal cations, and on multiply H-bonded complexes. We also comment on the involvement of polarization, a key contributor to non-additivity, in the issues of multipole transferability and conjugation. In the last section we provide recent examples of APMM validations by QC, which relate to interactions taking place in the recognition sites of kinases and metalloproteins. We conclude by mentioning prospects of extensive applications of APMM.
Approaching the double-faceted nature of the CX bond in halobenzenes with a bifunctional probe
Chemical Physics Letters, 2015
ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along th... more ABSTRACT In halobenzenes, the CX bond (X = Cl, Br) is doubly faceted, electron-deficient along the CX direction, and electron-rich on its flanks. We have recently shown that both features could be enhanced by appropriate electron-withdrawing and electron-donating groups, respectively. In this paper we further highlight this dual character by approaching a bifunctional probe, N-methylformamide, to both regions in representative substituted halobenzenes. We report the results of interaction energy computations, ELF, and NCI analyses. These methods used in conjunction show the responsiveness of the CX bond to both kinds of substitutions, enabling significant interaction energy gains with respect to the parent compound.
Stacked and H-bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics
The journal of physical chemistry. B, Jan 29, 2015
Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well... more Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds on nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of non-canonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on fourteen stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for...
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Papers by Jean-Philip Piquemal