Methodology Publications:

MD Integrators

Pushing the Limits of Multiple-Time-Step Strategies for Polarizable Point Dipole Molecular Dynamics, L. Lagardere, F. Aviat and J.-P. Piquemal, J. Phys. Chem. Lett., 10, 2593-2599 (2019)

Exchange Repulsion

Classical Pauli Repulsion: An Anisotropic, Atomic Multipole Model, J. A. Rackers and J. W. Ponder, J. Chem. Phys., 150, 084104 (2019)


A Physically Grounded Damped Dispersion Model with Particle Mesh Ewald Summation, J. A. Rackers, C. Liu, P. Ren and J. W. Ponder, J. Chem. Phys., 149, 084115 (2018)

Induced Dipoles

Truncated Conjugated Gradient (TCG): An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations, F. Aviat, A. Levitt, B. Stamm, Y. Maday, P. Ren, J. W. Ponder, L. Lagardere and J.-P. Piquemal, J. Chem. Theory Comput., 13, 180-190 (2017)
An Empirical Extrapolation Scheme for Efficient Treatment of Induced Dipoles, A. C. Simmonett, F. C. Pickard IV, J. W. Ponder and B. R. Brooks, J. Chem. Phys., 145, 164101 (2016)

Charge Penetration

An Optimized Charge Penetration Model for Use with the AMOEBA Force Field, J. A. Rackers, Q. Wang, C. Liu, J.-P. Piquemal, P. Ren and J. W. Ponder, Phys. Chem. Chem. Phys., 19, 276-291 (2017)
Scalable Improvement of SPME Multipolar Electrostatics in Anisotropic Polarizable Molecular Mechanics Using a General Short-Range Penetration Correction up to Quadrupoles, C. Narth, L. Lagardere, E. Polack, N. Gresh, Q. Wang, D. R. Bell, J. A. Rackers, J. W. Ponder, P. Y. Ren and J.-P. Piquemal, J. Comput. Chem., 37, 494-506 (2016)
General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field, Q. Wang, J. A. Rackers, C. He, R. Qi, C. Narth, L. Lagardere, N. Gresh, J. W. Ponder, J.-P. Piquemal and P. Ren, J. Chem. Theory Comput., 11, 2609-2618 (2015)

Geometry-Dependent Charge Flux

Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential, C. Liu, J.-P. Piquemal, P. Ren, J. Phys. Chem. Lett., 11, 419–426 (2020)

Ligand Field Effects

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field, J. Y. Xiang and J. W. Ponder, J. Chem. Theory Comput., 10, 298-311 (2014)
A Valence Bond Model for Aqueous Cu(II) and Zn(II) Ions in the AMOEBA Polarizable Force Field, J. Y. Xiang and J. W. Ponder, J. Comput. Chem., 34, 739-749 (2013)
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