Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations Albaugh A, Head-Gordon T. 2017. A New Method for Treating Drude Polarization in Classical Molecular Simulation, J Chem Phys Journal of Chemical Theory and Computation, vol.147, issue.13, pp.5207-5223, 2017. ,
Accurate Classical Polarization Solution with No Self-Consistent Field Iterations, The Journal of Physical Chemistry Letters, vol.8, issue.8, pp.1714-1737, 2017. ,
DOI : 10.1021/acs.jpclett.7b00450
Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations, Journal of Chemical Theory and Computation, vol.13, issue.1, pp.180-90, 2017. ,
DOI : 10.1021/acs.jctc.6b00981
URL : https://hal.archives-ouvertes.fr/hal-01395833
Calculating binding free energies of host???guest systems using the AMOEBA polarizable force field, Physical Chemistry Chemical Physics, vol.100, issue.44, pp.30261-69, 2016. ,
DOI : 10.1103/PhysRevLett.100.020603
URL : http://europepmc.org/articles/pmc5102783?pdf=render
Mesh-free hierarchical clustering methods for fast evaluation of electrostatic interactions of point multipoles, The Journal of Chemical Physics, vol.4, issue.16, p.164104, 2017. ,
DOI : 10.1002/jcc.20290
Short-Range Interactions of Concentrated Proline in Aqueous Solution, The Journal of Physical Chemistry B, vol.118, issue.49, pp.14267-77, 2014. ,
DOI : 10.1021/jp508779d
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations, Journal of Computational Chemistry, vol.36, pp.1990-2008, 2015. ,
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization, The Journal of Physical Chemistry B, vol.117, issue.8, pp.2328-2366, 2013. ,
DOI : 10.1021/jp311851r
URL : http://europepmc.org/articles/pmc3622952?pdf=render
QTPIE: Charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics, Chemical Physics Letters, vol.438, issue.4-6, pp.315-335, 2007. ,
DOI : 10.1016/j.cplett.2007.02.065
Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures, The Journal of Chemical Physics, vol.15, issue.4, p.244107, 2011. ,
DOI : 10.1103/PhysRev.165.201
URL : http://europepmc.org/articles/pmc3143679?pdf=render
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases, Journal of Computational Chemistry, vol.20, issue.10, pp.1048-57, 2001. ,
DOI : 10.1021/bi00514a006
, Classical Electrostatics for Biomolecular Simulations. Chemical Reviews, vol.114, pp.779-814, 2014.
Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A, The Journal of Physical Chemistry B, vol.113, issue.27, pp.9183-96, 2009. ,
DOI : 10.1021/jp901088g
Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model, Journal of Chemical Theory and Computation, vol.12, issue.8, pp.3926-3973, 2016. ,
DOI : 10.1021/acs.jctc.6b00567
Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations, The Journal of Chemical Physics, vol.84, issue.2, p.161721, 2017. ,
DOI : 10.1021/ct600180x
Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations, Nature Communications Journal of Chemical Theory and Computation, vol.7, issue.10, pp.12753-12771, 2014. ,
Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials, Journal of Chemical Theory and Computation, vol.12, issue.8, pp.3491-505, 2016. ,
DOI : 10.1021/acs.jctc.6b00397
OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics. bioRxiv 21 Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds, Journal of Computational Chemistry, vol.34, pp.1125-1160, 2013. ,
Perspective: Computer simulations of long time dynamics, The Journal of Chemical Physics, vol.144, issue.6, p.60901, 2016. ,
DOI : 10.1103/PhysRevLett.35.789
Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field, Physical Chemistry Chemical Physics, vol.150, issue.7, pp.5579-90, 2017. ,
DOI : 10.1039/c1fd00004g
Computing time scales from reaction coordinates by milestoning, The Journal of Chemical Physics, vol.126, issue.23, pp.10880-89, 2004. ,
DOI : 10.1007/BF01016796
LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields, Journal of Computational Chemistry, vol.37, pp.1019-1048, 2016. ,
Improved Polarizable Dipole???Dipole Interaction Model for Hydrogen Bonding, Stacking, T-Shaped, and X???H???????? Interactions, Journal of Chemical Theory and Computation, vol.13, issue.6, pp.2730-2771, 2017. ,
DOI : 10.1021/acs.jctc.6b00936
Multipolar Ewald Methods, 1: Theory, Accuracy, and Performance, Journal of Chemical Theory and Computation, vol.11, issue.2, pp.436-50, 2015. ,
DOI : 10.1021/ct5007983
URL : https://doi.org/10.1021/ct5007983
Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations, Journal of Chemical Theory and Computation, vol.10, issue.3, pp.1326-1366, 2014. ,
DOI : 10.1021/ct4009969
Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes, Annual Review of Biophysics, vol.45, issue.1, pp.253-78, 2016. ,
DOI : 10.1146/annurev-biophys-062215-011113
URL : http://europepmc.org/articles/pmc5526348?pdf=render
QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential, The Journal of Physical Chemistry Letters, vol.9, issue.11, pp.3062-67, 2018. ,
DOI : 10.1021/acs.jpclett.8b01412
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand???Macromolecule Complexes. A Bottom-Up Strategy, Journal of Chemical Theory and Computation, vol.3, issue.6, pp.1960-86, 2007. ,
DOI : 10.1021/ct700134r
URL : https://hal.archives-ouvertes.fr/hal-00494588
Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown, Journal of Computational Chemistry, vol.37, issue.32, pp.2770-82, 2016. ,
DOI : 10.1002/jcc.24375
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, vol.119, issue.30, pp.9477-95, 2015. ,
DOI : 10.1021/acs.jpcb.5b01695
URL : https://hal.archives-ouvertes.fr/hal-01287484
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, vol.119, issue.30, pp.9477-95, 2015. ,
DOI : 10.1021/acs.jpcb.5b01695
URL : https://hal.archives-ouvertes.fr/hal-01287484
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field, Journal of the American Chemical Society, vol.125, issue.50, pp.15671-82, 2003. ,
DOI : 10.1021/ja037005r
Polarizable force fields, Current Opinion in Structural Biology, vol.11, issue.2, pp.236-278, 2001. ,
DOI : 10.1016/S0959-440X(00)00196-2
Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs, Journal of Computational Chemistry, vol.71, issue.23, pp.2047-55, 2017. ,
DOI : 10.1016/S0006-3495(96)79267-6
URL : https://hal.archives-ouvertes.fr/hal-01571313
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks, Journal of Computational Chemistry, vol.424, issue.2, 2018. ,
DOI : 10.1016/j.cplett.2006.04.035
Mapping the Drude polarizable force field onto a multipole and induced dipole model Markov State Models: From an Art to a Science, The Journal of Chemical Physics Journal of the American Chemical Society, vol.147, issue.140, pp.2386-96, 2017. ,
Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space, Journal of Chemical Theory and Computation, vol.10, issue.12, pp.5493-504, 2014. ,
DOI : 10.1021/ct500803r
Searching the Force Field Electrostatic Multipole Parameter Space, Journal of Chemical Theory and Computation, vol.12, issue.4, pp.1824-1856, 2016. ,
DOI : 10.1021/acs.jctc.5b01187
Calculation of protein-ligand binding free energy by using a polarizable potential, Proceedings of the National Academy of Sciences, vol.99, issue.7, pp.6290-95, 2008. ,
DOI : 10.1021/ja00449a051
URL : http://www.pnas.org/content/105/17/6290.full.pdf
Conformational Interconversions of Amino Acid Derivatives, Journal of Chemical Theory and Computation, vol.12, issue.2, pp.694-705, 2016. ,
DOI : 10.1021/acs.jctc.5b00911
Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method, The Journal of Physical Chemistry B, vol.121, issue.17, pp.4319-4351, 2017. ,
DOI : 10.1021/acs.jpcb.6b12647
Computer Modeling of Halogen Bonds and Other ??-Hole Interactions, Chemical Reviews, vol.116, issue.9, pp.5155-87, 2016. ,
DOI : 10.1021/acs.chemrev.5b00560
Charge Anisotropy: Where Atomic Multipoles Matter Most, Journal of Chemical Theory and Computation, vol.10, issue.10, pp.4488-96, 2014. ,
DOI : 10.1021/ct5005565
QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin???Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches, Journal of Chemical Theory and Computation, vol.10, issue.6, pp.2615-2644, 2014. ,
DOI : 10.1021/ct500183w
Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process, The Journal of Physical Chemistry B, vol.119, issue.32, pp.10275-86, 2015. ,
DOI : 10.1021/acs.jpcb.5b01295
Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields, Chemical Science, vol.10, issue.132, pp.956-72, 2018. ,
DOI : 10.1021/ct500050p
URL : https://hal.archives-ouvertes.fr/hal-01648245
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model, The Journal of Physical Chemistry B, vol.119, issue.29, pp.9423-9460, 2015. ,
DOI : 10.1021/jp510896n
URL : http://europepmc.org/articles/pmc4772747?pdf=render
Induced Dipole???Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid ??-Peptides, The Journal of Physical Chemistry B, vol.119, issue.51, pp.15574-82, 2015. ,
DOI : 10.1021/acs.jpcb.5b09978
URL : https://doi.org/10.1021/acs.jpcb.5b09978
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications, Chemical Reviews, vol.116, issue.9, pp.4983-5013, 2016. ,
DOI : 10.1021/acs.chemrev.5b00505
URL : https://doi.org/10.1021/acs.chemrev.5b00505
Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics, Journal of Chemical Theory and Computation, vol.13, issue.5, pp.2053-71, 2017. ,
DOI : 10.1021/acs.jctc.7b00067
URL : https://doi.org/10.1016/j.bpj.2014.11.875
Induced Polarization Influences the Fundamental Forces in DNA Base Flipping, The Journal of Physical Chemistry Letters, vol.5, issue.12, pp.2077-83, 2014. ,
DOI : 10.1021/jz5009517
URL : https://doi.org/10.1021/jz5009517
Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models, The Journal of Chemical Physics, vol.141, issue.1, p.14103, 2014. ,
DOI : 10.1063/1.1669389
URL : http://europepmc.org/articles/pmc4106032?pdf=render
Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids, Journal of Chemical Theory and Computation, vol.13, issue.9, pp.4535-52, 2017. ,
DOI : 10.1021/acs.jctc.7b00262
URL : http://europepmc.org/articles/pmc5595662?pdf=render
Machine Learning Force Field Parameters from Ab Initio Data, Journal of Chemical Theory and Computation, vol.13, issue.9, pp.4492-503, 2017. ,
DOI : 10.1021/acs.jctc.7b00521
URL : http://europepmc.org/articles/pmc5931379?pdf=render
Molecular Dynamics Simulations, Journal of Chemical Theory and Computation, vol.14, issue.6, pp.2834-2876, 2018. ,
DOI : 10.1021/acs.jctc.7b01189
Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin, Journal of Molecular Modeling, vol.114, issue.4, p.2189, 2014. ,
DOI : 10.1021/jp104425t
Generalized and efficient algorithm for computing multipole energies and gradients based on Cartesian tensors, The Journal of Chemical Physics, vol.46, issue.11, p.114115, 2015. ,
DOI : 10.1137/110830125
URL : http://europepmc.org/articles/pmc4583518?pdf=render
Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator, Journal of Chemical Theory and Computation, vol.14, issue.2, pp.1083-98, 2018. ,
DOI : 10.1021/acs.jctc.7b01086
Effects of Polarizable Solvent Models upon the Relative Stability of an ??-Helical and a ??-Hairpin Structure of an Alanine Decapeptide, Journal of Chemical Theory and Computation, vol.11, issue.5, pp.1983-86, 2015. ,
DOI : 10.1021/acs.jctc.5b00210
Polarizable Molecular Dynamics in a Polarizable Continuum Solvent, Journal of Chemical Theory and Computation, vol.11, issue.2, pp.623-657, 2015. ,
DOI : 10.1021/ct500998q
URL : https://hal.archives-ouvertes.fr/hal-01114784
Polarization Force Field for Base Pairs with Amino Acid Residue Complexes, Journal of Chemical Theory and Computation, vol.13, issue.5, pp.2098-111, 2017. ,
DOI : 10.1021/acs.jctc.6b01206
Capturing Many-Body Interactions with Classical Dipole Induction Models, Journal of Chemical Theory and Computation, vol.13, issue.6, pp.2751-61, 2017. ,
DOI : 10.1021/acs.jctc.7b00225
URL : https://doi.org/10.1021/acs.jctc.7b00225
The Dynamic Origin of Color Tuning in Proteins Revealed by a Carotenoid Pigment, The Journal of Physical Chemistry Letters, vol.9, issue.9, pp.2404-2414, 2018. ,
DOI : 10.1021/acs.jpclett.8b00763
Hybrid QM/MM Molecular Dynamics with AMOEBA Polarizable Embedding, Journal of Chemical Theory and Computation, vol.13, issue.9, pp.4025-4058, 2017. ,
DOI : 10.1021/acs.jctc.7b00572
URL : https://hal.archives-ouvertes.fr/hal-01571619
A QM/MM Approach Using the AMOEBA Polarizable Embedding: From Ground State Energies to Electronic Excitations, Journal of Chemical Theory and Computation, vol.12, issue.8, pp.3654-61, 2016. ,
DOI : 10.1021/acs.jctc.6b00385
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator, Journal of Chemical Theory and Computation, vol.9, issue.12, pp.5430-5479, 2013. ,
DOI : 10.1021/ct400781b
URL : http://europepmc.org/articles/pmc3896220?pdf=render
Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method, Journal of Chemical Theory and Computation, vol.12, pp.41-52, 2016. ,
Polarizable force fields for molecular dynamics simulations of biomolecules, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.5, pp.241-54, 2015. ,
Electrostatic Polarization Is Crucial for Reproducing pKa Shifts of Carboxylic Residues in Turkey Ovomucoid Third Domain, The Journal of Physical Chemistry B, vol.111, issue.30, pp.9036-9080, 2007. ,
DOI : 10.1021/jp071284d
, The Journal of Physical Chemistry B, vol.102, issue.18, pp.3586-616, 1998.
DOI : 10.1021/jp973084f
binding to an amide plane, Physical Chemistry Chemical Physics, vol.54, issue.5, pp.4191-200, 2016. ,
DOI : 10.1021/acs.biochem.5b01000
Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study, ChemPhysChem, vol.16, pp.658-65, 2015. ,
Assessing Ion???Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations, Journal of Chemical Theory and Computation, vol.12, issue.11, pp.5422-5459, 2016. ,
DOI : 10.1021/acs.jctc.6b00764
A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps, Journal of Chemical Theory and Computation, vol.12, issue.5, pp.2170-80, 2016. ,
DOI : 10.1021/acs.jctc.6b00188
Limiting assumptions in molecular modeling: electrostatics, Journal of Computer-Aided Molecular Design, vol.133, issue.45, pp.107-121, 2013. ,
DOI : 10.1021/ja207470h
Density Functional Theory Study on the Interactions of Metal Ions with Long Chain Deprotonated Carboxylic Acids, The Journal of Physical Chemistry A, vol.119, issue.40, pp.10195-203, 2015. ,
DOI : 10.1021/acs.jpca.5b04136
Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions, The Journal of Physical Chemistry A, vol.119, issue.22, pp.5865-82, 2015. ,
DOI : 10.1021/acs.jpca.5b03159
Distributed Multipoles from a Robust Basis-Space Implementation of the Iterated Stockholder Atoms Procedure, Journal of Chemical Theory and Computation, vol.10, issue.12, pp.5405-5423, 2014. ,
DOI : 10.1021/ct5008444
Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances, The Journal of Chemical Physics, vol.134, issue.1, p.14103, 2011. ,
DOI : 10.1002/prot.340210403
The impact of molecular dynamics on drug design: applications for the characterization of ligand???macromolecule complexes, Drug Discovery Today, vol.20, issue.6, pp.686-702, 2015. ,
DOI : 10.1016/j.drudis.2015.01.003
Modeling Organochlorine Compounds and the ??-Hole Effect Using a Polarizable Multipole Force Field, The Journal of Physical Chemistry B, vol.118, issue.24, pp.6456-65, 2014. ,
DOI : 10.1021/jp411671a
URL : http://doi.org/10.1021/jp411671a
Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals, Physical Chemistry Chemical Physics, vol.338, issue.44, pp.30313-30335, 2016. ,
DOI : 10.1126/science.1219021
URL : http://europepmc.org/articles/pmc5102770?pdf=render
Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins, Journal of Chemical Theory and Computation, vol.11, issue.10, pp.4992-5001, 2015. ,
DOI : 10.1021/acs.jctc.5b00524
URL : https://doi.org/10.1021/acs.jctc.5b00524
Massively Parallel Implementation of Divide-and-Conquer Jacobi Iterations Using Particle-Mesh Ewald for Force Field Polarization Advanced models for water simulations, e1355 90. Ouyang JF, Bettens RP. 2016. When are Many-Body Effects Significant, pp.5860-67, 2018. ,
DOI : 10.1021/acs.jctc.8b00328
Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections, Journal of Chemical Theory and Computation, vol.12, issue.6, pp.2973-82, 2016. ,
DOI : 10.1021/acs.jctc.6b00128
Polarization effects in molecular mechanical force fields Current Status of the AMOEBA Polarizable Force Field, Journal of Physics: Condensed Matter The Journal of Physical Chemistry B, vol.21, issue.114, pp.333102-93, 2009. ,
Elucidating the Phosphate Binding Mode of PBP: The Critical Effect of Buffer Solution, The Journal of Physical Chemistry B, vol.95, 2018. ,
United polarizable multipole water model for molecular mechanics simulation, The Journal of Chemical Physics, vol.143, issue.1, p.14504, 2015. ,
DOI : 10.1021/ct4003702
URL : http://europepmc.org/articles/pmc4499046?pdf=render
General van der Waals potential for common organic molecules, Bioorganic & Medicinal Chemistry, vol.24, issue.20, pp.4911-4930, 2016. ,
DOI : 10.1016/j.bmc.2016.07.062
URL : http://europepmc.org/articles/pmc5360186?pdf=render
Molecular mechanism of Zn<sup>2+</sup> inhibition of a voltage-gated proton channel An optimized charge penetration model for use with the AMOEBA force field, Proceedings of the National Academy of Sciences Physical Chemistry Chemical Physics, vol.113, issue.19, pp.5962-71, 2016. ,
UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations, Journal of the American Chemical Society, vol.114, issue.25, pp.10024-10059, 1992. ,
DOI : 10.1021/ja00051a040
Biomolecular electrostatics and solvation: a computational perspective, Quarterly Reviews of Biophysics, vol.27, issue.04, pp.427-91, 2012. ,
DOI : 10.1002/jcc.10120
URL : http://europepmc.org/articles/pmc3533255?pdf=render
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation, The Journal of Physical Chemistry B, vol.107, issue.24, pp.5933-5980, 2003. ,
DOI : 10.1021/jp027815+
URL : http://dasher.wustl.edu/ponder/papers/jpcb-107-5933-03.pdf
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules, Journal of Chemical Theory and Computation, vol.7, issue.10, pp.3143-61, 2011. ,
DOI : 10.1021/ct200304d
URL : http://europepmc.org/articles/pmc3196664?pdf=render
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald, Journal of Chemical Theory and Computation, vol.9, issue.9, pp.3878-88, 2013. ,
DOI : 10.1021/ct400314y
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations, Journal of Computational Chemistry, vol.25, pp.1-16, 2004. ,
Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2, The Journal of Physical Chemistry B, vol.115, issue.20, pp.6749-63, 2011. ,
DOI : 10.1021/jp201934p
URL : https://hal.archives-ouvertes.fr/hal-00764855
All-atom polarizable force field for DNA based on the classical drude oscillator model, Journal of Computational Chemistry, vol.16, issue.16, pp.1219-1258, 2014. ,
DOI : 10.1007/s00894-009-0572-4
URL : http://europepmc.org/articles/pmc4075971?pdf=render
on DNA Conformational Properties, The Journal of Physical Chemistry Letters, vol.6, issue.1, pp.212-228, 2015. ,
DOI : 10.1021/jz5024543
The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field, Journal of Chemical Theory and Computation, vol.8, issue.5, pp.1721-1757, 2012. ,
DOI : 10.1021/ct300035u
, Journal of Chemical Theory and Computation, vol.9, issue.7, pp.3062-71, 2013.
DOI : 10.1021/ct400237r
The ReaxFF reactive force-field: development, applications and future directions, npj Computational Materials, vol.134, issue.1, p.15011, 2016. ,
DOI : 10.1021/ja209152n
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins, Journal of Chemical Theory and Computation, vol.9, issue.9, pp.4046-63, 2013. ,
DOI : 10.1021/ct4003702
An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald, The Journal of Chemical Physics, vol.4, issue.18, p.184101, 2014. ,
DOI : 10.1002/qua.560540202
An empirical extrapolation scheme for efficient treatment of induced dipoles, The Journal of Chemical Physics, vol.4, issue.16, p.164101, 2016. ,
DOI : 10.1021/acs.jctc.5b00171
The critical effect of polarization on the dynamical structure of guanine quadruplex DNA, Physical Chemistry Chemical Physics, vol.116, issue.11, pp.3846-54, 2013. ,
DOI : 10.1021/jp3019759
Development of AMOEBA Force Field for 1,3-Dimethylimidazolium Based Ionic Liquids, The Journal of Physical Chemistry B, vol.118, issue.25, pp.7156-66, 2014. ,
DOI : 10.1021/jp503347f
Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function, The Journal of Chemical Physics, vol.247, issue.5, pp.2237-51, 2001. ,
DOI : 10.1063/1.443323
The Theory of Intermolecular Forces Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field, The Journal of Physical Chemistry Letters, vol.118, issue.8, pp.901-909, 2016. ,
Accounting for Polarization Cost When Using Fixed Charge Force Fields. I. Method for Computing Energy, The Journal of Physical Chemistry B, vol.114, issue.26, pp.8621-8651, 2010. ,
DOI : 10.1021/jp911699p
based force field for aqueous ions, The Journal of Chemical Physics, vol.77, issue.11, p.114507, 2012. ,
DOI : 10.1038/nmat2422
URL : https://hal.archives-ouvertes.fr/hal-01897599
transport, Chemical Science, vol.5, issue.9, pp.6230-6268, 2017. ,
DOI : 10.1038/srep10657
Minimal distributed charges: Multipolar quality at the cost of point charge electrostatics, The Journal of Chemical Physics, vol.147, issue.16, p.161712, 2017. ,
DOI : 10.1063/1.1630791
New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy, Journal of Chemical Theory and Computation, vol.14, issue.2, pp.739-58, 2018. ,
DOI : 10.1021/acs.jctc.7b00851
Iodide Binding in Sodium-Coupled Cotransporters, Journal of Chemical Information and Modeling, vol.57, issue.12, pp.3043-55, 2017. ,
DOI : 10.1021/acs.jcim.7b00521
Direct computation of parameters for accurate polarizable force fields, The Journal of Chemical Physics, vol.4, issue.19, 2014. ,
DOI : 10.1007/BF02708340
A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities, Phys. Chem. Chem. Phys., vol.105, issue.33, pp.17857-62, 2014. ,
DOI : 10.1063/1.472823
QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation, Journal of Chemical Theory and Computation, vol.8, issue.10, pp.3839-53, 2012. ,
DOI : 10.1021/ct300085z
Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials, Chemical Reviews, vol.117, issue.20, pp.12641-704, 2017. ,
DOI : 10.1021/acs.chemrev.7b00139
Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory, The Journal of Chemical Physics, vol.144, issue.22, p.224107, 2016. ,
DOI : 10.1021/ja00074a030
Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization, The Journal of Physical Chemistry B, vol.116, issue.24, pp.7088-101, 2012. ,
DOI : 10.1021/jp3019759
URL : http://europepmc.org/articles/pmc3391542?pdf=render
Development and testing of a general amber force field, Journal of Computational Chemistry, vol.17, issue.9, pp.1157-74, 2004. ,
DOI : 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
URL : http://amber.scripps.edu/antechamber/gaff.pdf
Systematic Improvement of a Classical Molecular Model of Water, The Journal of Physical Chemistry B, vol.117, issue.34, pp.9956-72, 2013. ,
DOI : 10.1021/jp403802c
URL : http://europepmc.org/articles/pmc3770532?pdf=render
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15, The Journal of Physical Chemistry B, vol.121, issue.16, pp.4023-4062, 2017. ,
DOI : 10.1021/acs.jpcb.7b02320
General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field, Journal of Chemical Theory and Computation, vol.11, issue.6, pp.2609-2627, 2015. ,
DOI : 10.1021/acs.jctc.5b00267
URL : https://hal.archives-ouvertes.fr/hal-01287207
Polarizable Force Fields:?? History, Test Cases, and Prospects, Journal of Chemical Theory and Computation, vol.3, issue.6, pp.2034-2079, 2007. ,
DOI : 10.1021/ct700127w
Multiensemble Markov models of molecular thermodynamics and kinetics, Proceedings of the National Academy of Sciences, 2016. ,
DOI : 10.1214/aos/1176346585
URL : http://www.pnas.org/content/113/23/E3221.full.pdf
Automation of AMOEBA polarizable force field parameterization for small molecules, Theoretical Chemistry Accounts, vol.110, issue.32, p.1138, 2012. ,
DOI : 10.1021/jp063552y
URL : http://europepmc.org/articles/pmc3322661?pdf=render
AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms, Journal of Chemical Theory and Computation, vol.14, issue.5, pp.2705-2725, 2018. ,
DOI : 10.1021/acs.jctc.7b01128
Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor, The Journal of Chemical Physics, vol.145, issue.16, p.164110, 2016. ,
DOI : 10.1021/ct4003702
Polarizable and Non-Polarizable Force Field Representations of Ferric Cation and Validations, The Journal of Physical Chemistry B, vol.121, issue.23, pp.5718-5747, 2017. ,
DOI : 10.1021/acs.jpcb.7b02010
A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field, Journal of Computational Chemistry, vol.249, issue.9, pp.739-788, 2013. ,
DOI : 10.1016/j.ccr.2005.03.032
Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEM???? fluctuating charge force field, Journal of Computational Chemistry, vol.71, issue.23, 2014. ,
DOI : 10.6023/A13060606
Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics, The Journal of Physical Chemistry B, vol.119, issue.32, pp.10145-55, 2015. ,
DOI : 10.1021/acs.jpcb.5b04262
URL : http://europepmc.org/articles/pmc4664157?pdf=render
Microscopic mechanisms that govern the titration response and pKa values of buried residues in staphylococcal nuclease mutants, Proteins: Structure, Function, and Bioinformatics, vol.85, pp.268-81, 2017. ,
Analytic energy gradient of excited electronic state within TDDFT/MMpol framework: Benchmark tests and parallel implementation, The Journal of Chemical Physics, vol.143, issue.13, p.134104, 2015. ,
DOI : 10.1021/ct501087m
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids, Journal of Chemical Theory and Computation, vol.14, issue.4, pp.2084-108, 2018. ,
DOI : 10.1021/acs.jctc.7b01169
Entropy and Polarity Control the Partition and Transportation of Drug-like Molecules in Biological Membrane, Scientific Reports, vol.30, issue.1, p.17749, 2017. ,
DOI : 10.1021/jm00390a002