Related references
Note: Only part of the references are listed.An Overview of Electrostatic Free Energy Computations for Solutions and Proteins
Yen-Lin Lin et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Net Charge Changes in the Calculation of Relative Ligand-Binding Free Energies via Classical Atomistic Molecular Dynamics Simulation
Maria M. Reif et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
Truncation Effects of Shift Function Methods in Bulk Water Systems
Kazuaki Z. Takahashi
ENTROPY (2013)
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
Gabriel J. Rocklin et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
A Case Study of Truncated Electrostatics for Simulation of Polyelectrolyte Brushes on GPU Accelerators
Trung Dac Nguyen et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics
Michel Masella et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions
Shaozhong Deng et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2013)
Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations
Frithjof Godschalk et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2013)
Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model
Shen Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)
Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation
Nathan Schmid et al.
COMPUTER PHYSICS COMMUNICATIONS (2012)
Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH
Jason A. Wallace et al.
JOURNAL OF CHEMICAL PHYSICS (2012)
A long-range electrostatic potential based on the Wolf method charge-neutral condition
Yasushige Yonezawa
JOURNAL OF CHEMICAL PHYSICS (2012)
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations
Jens Kleinjung et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors
Anita de Ruiter et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations
Bjoern Dahlgren et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
Maria M. Reif et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations
Stefano Piana et al.
PLOS ONE (2012)
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
Rio Yokota et al.
COMPUTER PHYSICS COMMUNICATIONS (2011)
A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent
Jason A. Wagoner et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Pairwise Long-Range Compensation for Strongly Ionic Systems
Seyit Kale et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Improving the description of salt bridge strength and geometry in a Generalized Born model
Yi Shang et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2011)
Physical Modeling of Aqueous Solvation
Christopher J. Fennell et al.
JOURNAL OF STATISTICAL PHYSICS (2011)
Long ranged interactions in computer simulations and for quasi-2D systems
Martial Mazars
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS (2011)
Assessing group-based cutoffs and the Ewald method for electrostatic interactions in clusters and in saturated, superheated, and supersaturated vapor phases of dipolar molecules
Mohammadhasan Dinpajooh et al.
THEORETICAL CHEMISTRY ACCOUNTS (2011)
Desolvation Costs of Salt Bridges across Protein Binding Interfaces: Similarities and Differences between Implicit and Explicit Solvent Models
Reza Salari et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2010)
Roles of Boundary Conditions in DNA Simulations: Analysis of Ion Distributions with the Finite-Difference Poisson-Boltzmann Method
Xiang Ye et al.
BIOPHYSICAL JOURNAL (2009)
Molecular dynamics simulations in a NpT ensemble using non-periodic boundary conditions
Giuseppe Brancato et al.
CHEMICAL PHYSICS LETTERS (2009)
Time-reversible molecular dynamics algorithms with bond constraints
Soren Toxvaerd et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
M. J. Harvey et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers
Richard M. Venable et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions
Maria M. Reif et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Multilevel summation of electrostatic potentials using graphics processing units
David J. Hardy et al.
PARALLEL COMPUTING (2009)
Recent advances in implicit solvent-based methods for biomolecular simulations
Jianhan Chen et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)
Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
Yuqing Deng et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
On the origin of the electrostatic potential difference at a liquid-vacuum interface
Edward Harder et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
Michele Cascella et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics
Vincent Kraeutler et al.
MOLECULAR SIMULATION (2008)
Treatment of charge singularities in implicit solvent models
Weihua Geng et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer
Arnau Cordomi et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions
Kasper P. Jensen et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
Dynamical motions of lipids and a finite size effect in simulations of bilayers
Jeffery B. Klauda et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics
Christopher J. Fennell et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Liquid water simulation: A critical examination of cutoff length
Yoshiteru Yonetani
JOURNAL OF CHEMICAL PHYSICS (2006)
Effective computer simulation of strongly coupled Coulomb fluids
ES Yakub
JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL (2006)
Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides
Luca Monticelli et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2006)
Electrostatics calculations: latest methodological advances
P Koehl
CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)
Influence of long-range electrostatic treatments on the folding of the N-terminal H4 histone tail peptide
RD Lins et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
The origin of layer structure artifacts in simulations of liquid water
D van der Spoel et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2006)
On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini
MA Villarreal et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2005)
Noise-driven numerical irreversibility in molecular dynamics technique
N Komatsu et al.
COMPUTER PHYSICS COMMUNICATIONS (2005)
Modified Wolf electrostatic summation: Incorporating an empirical charge overlap
Y Ma et al.
MOLECULAR SIMULATION (2005)
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations -: art. no. 034107
TN Heinz et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
A new method for computation of long ranged Coulomb forces in computer simulation of disordered systems
E Yakub et al.
JOURNAL OF LOW TEMPERATURE PHYSICS (2005)
A severe artifact in simulation of liquid water using a long cut-off length: Appearance of a strange layer structure
Y Yonetani
CHEMICAL PHYSICS LETTERS (2005)
Improving implicit solvent simulations: a Poisson-centric view
NA Baker
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
Evaluation of poisson solvation models using a hybrid explicit/implicit solvent method
MS Lee et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
DAC Beck et al.
BIOCHEMISTRY (2005)
Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions
M Patra et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Angular resolution and range of dipole-dipole correlations in water
G Mathias et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods
MA Kastenholz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Numerical irreversibility in time-reversible molecular dynamics simulation
N Komatsu et al.
PHYSICA D-NONLINEAR PHENOMENA (2004)
The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides
L Monticelli et al.
THEORETICAL CHEMISTRY ACCOUNTS (2004)
Molecular dynamics simulation of highly charged proteins:: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions
R Gargallo et al.
PROTEIN SCIENCE (2003)
A fast-Fourier transform method to solve continuum-electrostatics problems with truncated electrostatic interactions:: Algorithm and application to ionic solvation and ion-ion interaction
C Peter et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
An efficient method for computation of long-ranged Coulomb forces in computer simulation of ionic fluids
E Yakub et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions:: A continuum electrostatics study
M Bergdorf et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Calculation of ionic charging free energies in simulation systems with atomic charges, dipoles, and quadrupoles
DH Herce et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Analysis of the effect of electrostatic energy truncation in molecular dynamics simulations of immunoglobulin G light chain dimer
M Król
JOURNAL OF MOLECULAR MODELING (2003)
Methodological issues in lipid bilayer simulations
C Anézo et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water
G Mathias et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Molecular dynamics simulations of lipid bilayers:: Major artifacts due to truncating electrostatic interactions
M Patra et al.
BIOPHYSICAL JOURNAL (2003)
Enhancement of the wolf damped Coulomb potential: Static, dynamic, and dielectric properties of liquid water from molecular simulation
D Zahn et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2002)
Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?
RH Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
P Mark et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Molecular dynamics simulations of a double unit cell in a protein crystal:: Volume relaxation at constant pressure and correlation of motions between the two unit cells
R Walser et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
Novel generalized Born methods
MS Lee et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Derivation of an improved simple point charge model for liquid water:: SPC/A and SPC/L
A Glättli et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Solving the Poisson equation for solute-solvent systems using fast Fourier transforms
C Peter et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Molecular dynamics of the tRNAAla acceptor stem:: Comparison between continuum reaction field and particle-mesh Ewald electrostatic treatments
M Nina et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2002)
On the charge and molecule based summations of solvent electrostatic potentials and the validity of electrostatic linear response in water
CS Babu et al.
JOURNAL OF BIOLOGICAL PHYSICS (2002)
Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal
R Walser et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2001)
Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association
X Rozanska et al.
JOURNAL OF CHEMICAL PHYSICS (2000)
Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions:: Influence of artificial periodicity on peptide conformation
W Weber et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2000)
On the truncation of long-range electrostatic interactions in DNA
J Norberg et al.
BIOPHYSICAL JOURNAL (2000)