Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

(2015) K. Vanommeslaeghe et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem

(2014) Chad W. Hopkins et al.   Journal of Chemical Information and Modeling

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

All-atom polarizable force field for DNA based on the classical drude oscillator model

(2014) Alexey Savelyev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

(2014) Xiaojiao Mu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

(2014) Jiří Šponer et al.   Journal of Physical Chemistry Letters

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

(2013) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Effective fragment potential method inQ-CHEM: A guide for users and developers

(2013) Debashree Ghosh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Origin and Nature of Bond Rotation Barriers: A Unified View

(2013) Shubin Liu   JOURNAL OF PHYSICAL CHEMISTRY A

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

(2012) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

Toward a Unified Modeling of Environment and Bridge-Mediated Contributions to Electronic Energy Transfer: A Fully Polarizable QM/MM/PCM Approach

(2012) Stefano Caprasecca et al.   Journal of Chemical Theory and Computation

Optimization of the OPLS-AA Force Field for Long Hydrocarbons

(2012) Shirley W. I. Siu et al.   Journal of Chemical Theory and Computation

Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization

(2012) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of Polarizable Models for Molecular Mechanical Calculations. 3. Polarizable Water Models Conforming to Thole Polarization Screening Schemes

(2012) Jun Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automation of AMOEBA polarizable force field parameterization for small molecules

(2012) Johnny C. Wu et al.   THEORETICAL CHEMISTRY ACCOUNTS

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

(2011) Mark S. Gordon et al.   CHEMICAL REVIEWS

Accurate Intermolecular Potentials with Physically Grounded Electrostatics

(2011) Maxim Tafipolsky et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

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

(2011) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2011) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarization effects in molecular interactions

(2011) F. Javier Luque et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The polarizable point dipoles method with electrostatic damping: Implementation on a model system

(2010) Jonàs Sala et al.   JOURNAL OF CHEMICAL PHYSICS

Noncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method: Theory and Application to Nucleobase Oligomers

(2010) Debashree Ghosh et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Exploring Solvent Effects upon the Menshutkin Reaction Using a Polarizable Force Field

(2010) Orlando Acevedo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Erratum: Computational evidence that hyperconjugative interactions are not responsible for the anomeric effect

(2010) Yirong Mo   Nature Chemistry

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

(2010) Marie Zgarbová et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions

(2009) Fabien Archambault et al.   Journal of Chemical Theory and Computation

Contribution of the Intrinsic Mechanical Energy of the Phosphodiester Linkage to the Relative Stability of the A, BI, and BIIForms of Duplex DNA

(2009) Alexander D. MacKerell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarization effects in molecular mechanical force fields

(2009) Piotr Cieplak et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions

(2008) Dmitri V. Sakharov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An intramolecular induction correction model of the molecular dipole moment

(2007) Asbjørn Holt et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY