Classical Electrostatics for Biomolecular Simulations

Mapping Atomistic to Coarse-Grained Polymer Models Using Automatic Simplex Optimization To Fit Structural Properties

Reith, D., Meyer, H., & Müller-Plathe, F. (2001) · Macromolecules · doi:10.1021/ma001499k · Cited by 237

On the Truncation of Long-Range Electrostatic Interactions in DNA

Norberg, J., & Nilsson, L. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76405-8 · Cited by 236

A chemical potential equalization method for molecular simulations

York, D. M., & Yang, W. (1996) · The Journal of Chemical Physics · doi:10.1063/1.470886 · Cited by 233

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

Stansfeld, P. J., & Sansom, M. S. P. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct100569y · Cited by 231

Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry

Kaminski, G. A., Stern, H. A., Berne, B. J., & Friesner, R. A. (2004) · The Journal of Physical Chemistry A · doi:10.1021/jp0301103 · Cited by 230

Generalized solvent boundary potential for computer simulations

Im, W., Bernèche, S., & Roux, B. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1336570 · Cited by 229

Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations

Sagui, C., Pedersen, L. G., & Darden, T. A. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1630791 · Cited by 228

Development of a simple, self-consistent polarizable model for liquid water

Yu, H., Hansson, T., & van Gunsteren, W. F. (2003) · The Journal of Chemical Physics · doi:10.1063/1.1523915 · Cited by 224

The Origin of Layer Structure Artifacts in Simulations of Liquid Water

van der Spoel, D., & van Maaren, P. J. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct0502256 · Cited by 221

Design of a Next Generation Force Field: The X-POL Potential

Xie, W., & Gao, J. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct700167b · Cited by 218

A Fast Algorithm for Particle Simulations

Greengard, L., & Rokhlin, V. (1997) · Journal of Computational Physics · doi:10.1006/jcph.1997.5706 · Cited by 217

Propensity of soft ions for the air/water interface

Vrbka, L., Mucha, M., Minofar, B., Jungwirth, P., Brown, E. C., & Tobias, D. J. (2004) · Current Opinion in Colloid & Interface Science · doi:10.1016/j.cocis.2004.05.028 · Cited by 214

Electrostatic interactions in dissipative particle dynamics using the Ewald sums

González-Melchor, M., Mayoral, E., Velázquez, M. E., & Alejandre, J. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2400223 · Cited by 211

Efficient solution of Poisson’s equation with free boundary conditions

Genovese, L., Deutsch, T., Neelov, A., Goedecker, S., & Beylkin, G. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2335442 · Cited by 210

An Ewald summation method for planar surfaces and interfaces

Hautman, J., & Klein, M. L. (1992) · Molecular Physics · doi:10.1080/00268979200100301 · Cited by 210

Temperature and Pressure Dependence of the AMOEBA Water Model

Ren, P., & Ponder, J. W. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp0484332 · Cited by 209

Thermal Conductivities of Molecular Liquids by Reverse Nonequilibrium Molecular Dynamics

Zhang, M., Lussetti, E., de Souza, L. E. S., & Müller-Plathe, F. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp0512255 · Cited by 206

Virtual screening using molecular simulations

Yang, T., Wu, J. C., Yan, C., Wang, Y., Luo, R., Gonzales, M. B., Dalby, K. N., & Ren, P. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.23018 · Cited by 202

Ion sizes and finite-size corrections for ionic-solvation free energies

Hummer, G., Pratt, L. R., & García, A. E. (1997) · The Journal of Chemical Physics · doi:10.1063/1.475219 · Cited by 201

Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

Yu, H., & van Gunsteren, W. F. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1805516 · Cited by 200

Polarizability of molecular clusters as calculated by a dipole interaction model

Jensen, L., Åstrand, P.-O., Osted, A., Kongsted, J., & Mikkelsen, K. V. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1433747 · Cited by 199

Molecular dynamics with stochastic boundary conditions

Berkowitz, M., & McCammon, J. A. (1982) · Chemical Physics Letters · doi:10.1016/0009-2614(82)80028-6 · Cited by 195

N-particle dynamics of polarizable Stockmayer-type molecules

Vesely, F. J. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90028-6 · Cited by 194

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Piquemal, J.-P., Perera, L., Cisneros, G. A., Ren, P., Pedersen, L. G., & Darden, T. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2234774 · Cited by 194

Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions

Patra, M., Karttunen, M., Hyvönen, M. T., Falck, E., & Vattulainen, I. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp031281a · Cited by 194

Adaptively biased molecular dynamics for free energy calculations

Babin, V., Roland, C., & Sagui, C. (2008) · The Journal of Chemical Physics · doi:10.1063/1.2844595 · Cited by 192

Molecular dynamics computer simulation of surface properties of crystalline potassium chloride

Heyes, D. M., Barber, M., & Clarke, J. H. R. (1977) · Journal of the Chemical Society, Faraday Transactions 2 · doi:10.1039/f29777301485 · Cited by 191

Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models

Alper, H. E., & Levy, R. M. (1989) · The Journal of Chemical Physics · doi:10.1063/1.457198 · Cited by 190

Reconstruction of atomistic details from coarse‐grained structures

Rzepiela, A. J., Schäfer, L. V., Goga, N., Risselada, H. J., De Vries, A. H., & Marrink, S. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21415 · Cited by 190

Multiscale simulation of soft matter systems

Peter, C., & Kremer, K. (2010) · Faraday Discuss. · doi:10.1039/b919800h · Cited by 188

The Coordination of Uranyl in Water: A Combined Quantum Chemical and Molecular Simulation Study

Hagberg, D., Karlström, G., Roos, B. O., & Gagliardi, L. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0526719 · Cited by 187

Development of transferable interaction models for water. III. Reparametrization of an all-atom polarizable rigid model (TTM2–R) from first principles

Burnham, C. J., & Xantheas, S. S. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1423942 · Cited by 187

Strike a balance: Optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

Wang, Z., Zhang, W., Wu, C., Lei, H., Cieplak, P., & Duan, Y. (2006) · Journal of Computational Chemistry · doi:10.1002/jcc.20386 · Cited by 187

A New Coarse-Grained Model for Water: The Importance of Electrostatic Interactions

Wu, Z., Cui, Q., & Yethiraj, A. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp1019763 · Cited by 186

Ewald summation and reaction field methods for potentials with atomic charges, dipoles, and polarizabilities

Nymand, T. M., & Linse, P. (2000) · The Journal of Chemical Physics · doi:10.1063/1.481216 · Cited by 185

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method

Das, D., Eurenius, K. P., Billings, E. M., Sherwood, P., Chatfield, D. C., Hodošček, M., & Brooks, B. R. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1520134 · Cited by 185

Continuum Solvation Models: Classical and Quantum Mechanical Implementations

Cramer, C. J., & Truhlar, D. G. (1995) · Reviews in Computational Chemistry · doi:10.1002/9780470125830.ch1 · Cited by 184

Molecular Theories and Simulation of Ions and Polar Molecules in Water

Hummer, G., Pratt, L. R., & García, A. E. (1998) · The Journal of Physical Chemistry A · doi:10.1021/jp982195r · Cited by 182

Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations

van der Vegt, N., Peter, C., & Kremer, K. (2008) · Coarse-Graining of Condensed Phase and Biomolecular Systems · doi:10.1201/9781420059564.ch25 · Cited by 180

Ab Initio Quality Electrostatic Atomic and Molecular Properties Including Intermolecular Energies from a Transferable Theoretical Pseudoatom Databank

Volkov, A., Li, X., Koritsanszky, T., & Coppens, P. (2004) · The Journal of Physical Chemistry A · doi:10.1021/jp0379796 · Cited by 178

A Polarizable Intermolecular Potential Function for Simulation of Liquid Alcohols

Gao, J., Habibollazadeh, D., & Shao, L. (1995) · The Journal of Physical Chemistry · doi:10.1021/j100044a039 · Cited by 175

Isotropic periodic sum: A method for the calculation of long-range interactions

Wu, X., & Brooks, B. R. (2005) · The Journal of Chemical Physics · doi:10.1063/1.1836733 · Cited by 172

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations

Laino, T., Mohamed, F., Laio, A., & Parrinello, M. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct6001169 · Cited by 171

Characteristics of thermal conductivity in classical water models

Sirk, T. W., Moore, S., & Brown, E. F. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4789961 · Cited by 169

Solute diffusion in lipid bilayer membranes: An atomic level study by molecular dynamics simulation

Bassolino-Klimas, D., Alper, H. E., & Stouch, T. R. (1993) · Biochemistry · doi:10.1021/bi00210a010 · Cited by 168

Computation of charge-transfer energies by perturbation theory

Stone, A. J. (1993) · Chemical Physics Letters · doi:10.1016/0009-2614(93)80058-w · Cited by 167

Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility

Cerutti, D. S., Duke, R. E., Darden, T. A., & Lybrand, T. P. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct9001015 · Cited by 166

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

Wu, J. C., Piquemal, J.-P., Chaudret, R., Reinhardt, P., & Ren, P. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct100091j · Cited by 165

A generalization of the charge equilibration method for nonmetallic materials

Nistor, R. A., Polihronov, J. G., Müser, M. H., & Mosey, N. J. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2346671 · Cited by 164

Ewald summation of electrostatic multipole interactions up to the quadrupolar level

Aguado, A., & Madden, P. A. (2003) · The Journal of Chemical Physics · doi:10.1063/1.1605941 · Cited by 164

Automation of AMOEBA polarizable force field parameterization for small molecules

Wu, J. C., Chattree, G., & Ren, P. (2012) · Theoretical Chemistry Accounts · doi:10.1007/s00214-012-1138-6 · Cited by 163

Embedding a multideterminantal wave function in an orbital-free environment

Wesołowski, T. A. (2008) · Physical Review A · doi:10.1103/physreva.77.012504 · Cited by 160

Multiple grid methods for classical molecular dynamics

Skeel, R. D., Tezcan, I., & Hardy, D. J. (2002) · Journal of Computational Chemistry · doi:10.1002/jcc.10072 · Cited by 159

Setting up and optimization of membrane protein simulations

Faraldo‐Gómez, J. D., Smith, G. R., & Sansom, M. S. P. (2002) · European Biophysics Journal · doi:10.1007/s00249-002-0207-5 · Cited by 159

Biomolecular simulations at constant pH

Mongan, J., & Case, D. A. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.02.002 · Cited by 158

Effect of the treatment of long-range forces on the dynamics of ions in aqueous solutions

Perera, L., Essmann, U., & Berkowitz, M. L. (1995) · The Journal of Chemical Physics · doi:10.1063/1.469422 · Cited by 156

Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator

Lopes, P. E. M., Lamoureux, G., Roux, B., & MacKerell, A. D. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp0663614 · Cited by 155

Multiscale and Multiresolution Methods

Barth, T. J., Chan, T. F.-C., & Haimes, R. (2002) · Lecture notes in computational science and engineering · doi:10.1007/978-3-642-56205-1 · Cited by 153

Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

York, D. M., Yang, W., Lee, H., et al. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00122a034 · Cited by 153

Development of Polarizable Models for Molecular Mechanical Calculations I: Parameterization of Atomic Polarizability

Wang, J., Cieplak, P., Li, J., Hou, T., Luo, R., & Duan, Y. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp112133g · Cited by 153

Surface solvation of halogen anions in water clusters: An ab initio molecular dynamics study of the Cl−(H2O)6 complex

Tobias, D. J., Jungwirth, P., & Parrinello, M. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1360200 · Cited by 151

Ionic charging free energies: Spherical versus periodic boundary conditions

Darden, T., Pearlman, D. A., & Pedersen, L. G. (1998) · The Journal of Chemical Physics · doi:10.1063/1.477788 · Cited by 151

An ab initio study of water molecules in the bromide ion solvation shell

Raugei, S., & Klein, M. L. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1421366 · Cited by 148

Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations

Lin, H., & Truhlar, D. G. (2005) · The Journal of Physical Chemistry A · doi:10.1021/jp0446332 · Cited by 145

Molecular dynamics simulations of RNA: An in silico single molecule approach

McDowell, S. E., Špačková, N., Šponer, J., & Walter, N. G. (2006) · Biopolymers · doi:10.1002/bip.20620 · Cited by 144

Local Simulation Algorithms for Coulomb Interactions

Maggs, A. C., & Rossetto, V. (2002) · Physical Review Letters · doi:10.1103/physrevlett.88.196402 · Cited by 144

Selectivity in K + channels is due to topological control of the permeant ion's coordinated state

Bostick, D., & Brooks, C. L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700554104 · Cited by 139

Development of transferable interaction models for water. I. Prominent features of the water dimer potential energy surface

Burnham, C. J., & Xantheas, S. S. (2002) · The Journal of Chemical Physics · doi:10.1063/1.1423940 · Cited by 137

Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies

Wang, J., Cieplak, P., Li, J., Wang, J., Cai, Q., Hsieh, M., Lei, H., Luo, R., & Duan, Y. (2011) · The Journal of Physical Chemistry B · doi:10.1021/jp1121382 · Cited by 137

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

Baker, C. M., Lopes, P. E. M., Zhu, X., Roux, B., & MacKerell, A. D. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct9005773 · Cited by 132

Simulation and theory of electrostatic interactions in solution

Pratt, L. R., & Hummer, G. (1999) · Cited by 132

Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution.

Piquemal, J.-P., Gresh, N., & Giessner-Prettre, C. (2003) · Journal of Physical Chemistry A · doi:10.1021/jp035748t · Cited by 131

Coupling different levels of resolution in molecular simulations

Poblete, S., Praprotnik, M., Kremer, K., & Site, L. D. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3357982 · Cited by 130

Convergence of the Electrostatic Interaction Based on Topological Atoms

Popelier, P. L. A., Joubert, L., & Kosov, D. S. (2001) · The Journal of Physical Chemistry A · doi:10.1021/jp011511q · Cited by 130

Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency

Wang, H., Dommert, F., & Holm, C. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3446812 · Cited by 129

Summation of dipolar fields in simulated liquid-vapour interfaces

Lekner, J. (1989) · Physica A Statistical Mechanics and its Applications · doi:10.1016/0378-4371(89)90068-x · Cited by 128

Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics

Dixon, R. W., & Kollman, P. A. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199710)18:13<1632::aid-jcc5>3.0.co;2-s · Cited by 127

Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle

Fukuda, I., Yonezawa, Y., & Nakamura, H. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3582791 · Cited by 126

The limiting behavior of water hydrating a phospholipid monolayer: A computer simulation study

Alper, H., Bassolino‐Klimas, D., & Stouch, T. R. (1993) · The Journal of Chemical Physics · doi:10.1063/1.465947 · Cited by 125

Analysis and Evaluation of Channel Models: Simulations of Alamethicin

Tieleman, D. P., Hess, B., & Sansom, M. S. P. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75253-3 · Cited by 123

Understanding the dielectric properties of liquid amides from a polarizable force field.

Harder, E. D., Anisimov, V. M., Whitfield, T., MacKerell, A. D., & Roux, B. (2008) · Journal of Physical Chemistry B · doi:10.1021/jp709729d · Cited by 121

Electrical response in chemical potential equalization schemes

Chelli, R., Procacci, P., Righini, R., et al. (1999) · The Journal of Chemical Physics · doi:10.1063/1.480198 · Cited by 121

Importance of Explicit Salt Ions for Protein Stability in Molecular Dynamics Simulation

Ibragimova, G. T., & Wade, R. C. (1998) · Biophysical Journal · doi:10.1016/s0006-3495(98)77997-4 · Cited by 121

The effects of charge transfer on the properties of liquid water

Lee, A. J., & Rick, S. W. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3589419 · Cited by 120

A second generation distributed point polarizable water model

Kumar, R., Wang, F., Jenness, G. R., & Jordan, K. D. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3276460 · Cited by 120

Efficient and accurate three-dimensional Poisson solver for surface problems

Genovese, L., Deutsch, T., & Goedecker, S. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2754685 · Cited by 120

Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

Cisneros, G. A., Piquemal, J., & Darden, T. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2363374 · Cited by 118

The inverse problem in classical statistical mechanics

Chayes, J., Chayes, L., & Lieb, É. H. (1984) · Communications in Mathematical Physics · doi:10.1007/bf01218639 · Cited by 118

Computation of free energy profiles with parallel adaptive dynamics

Tony Lelièvre, A., Rousset, M., & Stoltz, G. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2711185 · Cited by 118

On the validity of the inverse conjecture in classical density functional theory

Chayes, J., & Chayes, L. (1984) · Journal of Statistical Physics · doi:10.1007/bf01010992 · Cited by 117

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.

Schaefer, P., Riccardi, D., & Cui, Q. (2005) · Journal of Chemical Physics · doi:10.1063/1.1940047 · Cited by 116

Stabilization energies of Cl−, Br−, and I− ions in water clusters

Perera, L., & Berkowitz, M. L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.466096 · Cited by 114

Recent advances in the study of nucleic acid flexibility by molecular dynamics

Orozco, M., Noy, A., & Pérez, A. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.01.005 · Cited by 113

Impact of cholesterol on voids in phospholipid membranes

Falck, E., Patra, M., Karttunen, M., Hyvönen, M. T., & Vattulainen, I. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1824033 · Cited by 112

A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution

Piquemal, J., Márquez, A. M., Parisel, O., & GIESSNER‐PRETTRE, C. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20242 · Cited by 111

Understanding Binding Affinity: A Combined Isothermal Titration Calorimetry/Molecular Dynamics Study of the Binding of a Series of Hydrophobically Modified Benzamidinium Chloride Inhibitors to Trypsin

Talhout, R., Villa, A., Mark, A. E., & Engberts, J. B. F. N. (2003) · Journal of the American Chemical Society · doi:10.1021/ja034676g · Cited by 109

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

Zhang, J., Yang, W. Y., Piquemal, J., & Ren, P. Y. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct200812y · Cited by 109

Combination of the exact potential and multipole methods (EP/MM) for evaluation of intermolecular electrostatic interaction energies with pseudoatom representation of molecular electron densities

Volkov, A. V., Koritsanszky, T. S., & Coppens, P. (2004) · Chemical Physics Letters · doi:10.1016/j.cplett.2004.04.097 · Cited by 108

Force Field Development and MD Simulations of Poly(ethylene oxide)/LiBF4 Polymer Electrolytes

Borodin, O. A., Smith, G. D., & Douglas, R. (2003) · The Journal of Physical Chemistry B · doi:10.1021/jp027539z · Cited by 107

Many-Body Polarization Effects and the Membrane Dipole Potential

Harder, E. D., MacKerell, A. D., & Roux, B. (2009) · Journal of the American Chemical Society · doi:10.1021/ja806825g · Cited by 106

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters

Yang, Z., Wu, Y., & Zhao, D. (2004) · The Journal of Chemical Physics · doi:10.1063/1.1640345 · Cited by 106

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

Xie, W., Pu, J., MacKerell, A. D., & Gao, J.-L. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct700146x · Cited by 104

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

Piana, S., Lindorff‐Larsen, K., Dirks, R. M., Salmon, J. K., Dror, R. O., & Shaw, D. E. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039918 · Cited by 103

Theoretical Characterization of the (H2O)21 Cluster: Application of an n-body Decomposition Procedure

Cui, J. X., Liu, H., & Jordan, K. D. (2006) · The Journal of Physical Chemistry B · doi:10.1021/jp056416m · Cited by 102

On the Structure of Ionic Liquids: Comparisons between Electronically Polarizable and Nonpolarizable Models I

Yan, T., Wang, Y., & Knox, C. K. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp9089112 · Cited by 102

Impact of cholesterol on voids in phospholipid membranes

Falck, E., Patra, M., Karttunen, M. M., et al. (2004) · TU/e Research Portal · Cited by 102

Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson–Boltzmann models

Wagoner, J. A., & Baker, N. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20089 · Cited by 101

Trypsin‐ligand binding free energies from explicit and implicit solvent simulations with polarizable potential

Jiao, D., Zhang, J., Duke, R. E., Li, G., Schnieders, M. J., & Ren, P. Y. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21268 · Cited by 101

Molecular dynamics simulation of polarizable water by an extended Lagrangian method

van Belle, D., Froeyen, M., Lippens, G., & Wodak, S. (1992) · Molecular Physics · doi:10.1080/00268979200102421 · Cited by 100

A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems

Zhou, R., & Berne, B. J. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470006 · Cited by 100

Atom charge transfer in molecular polarizabilities: application of the Olson-Sundberg model to aliphatic and aromatic hydrocarbons

Applequist, J. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100124a039 · Cited by 99

The electronegativity equalization method and the split charge equilibration applied to organic systems: Parametrization, validation, and comparison

Verstraelen, T., Speybroeck, V. V., & Waroquier, M. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3187034 · Cited by 97

Polarization and charge transfer in the hydration of chloride ions

Zhao, Z., Rogers, D. O. W., & Beck, T. L. (2010) · The Journal of Chemical Physics · doi:10.1063/1.3283900 · Cited by 97

Coarse-Graining in Interaction Space: A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials

Izvekov, S., Swanson, J. M. J., & Voth, G. A. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp710339n · Cited by 96

Theoretical Study of Aqueous Solvation of K+ Comparing ab Initio, Polarizable, and Fixed-Charge Models

Whitfield, T. W., Varma, S., Harder, E. D., Lamoureux, G., Rempe, S. B., & Roux, B. (2007) · Journal of Chemical Theory and Computation · doi:10.1021/ct700172b · Cited by 96

Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning

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P 3 M algorithm for dipolar interactions

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