Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide

(2014) Jing Huang et al.   BIOPHYSICAL JOURNAL

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

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

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

(2014) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator

(2014) Dhilon S. Patel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

(2014) Justin A. Lemkul et al.   Journal of Physical Chemistry Letters

Differential Impact of the Monovalent Ions Li+, Na+, K+, and Rb+ on DNA Conformational Properties

(2014) Alexey Savelyev et al.   Journal of Physical Chemistry Letters

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

(2014) Jing Huang et al.   Journal of Physical Chemistry Letters

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

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

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

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

New faster CHARMM molecular dynamics engine

(2013) Antti-Pekka Hynninen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

(2013) Janamejaya Chowdhary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D†

(2009) Anna-Pitschna E. Kunz et al.   JOURNAL OF PHYSICAL CHEMISTRY A

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY