(Q51126779)

English

Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: accelerating with advanced extrapolation of effective solvation forces.

scientific article published in December 2013

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: accelerating with advanced extrapolation of effective solvation forces. (English)

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

author name string

Igor Omelyan

1

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

Andriy Kovalenko

2

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

language of work or name

0 references

publication date

1 December 2013

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

Journal of Chemical Physics

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

139

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

24

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

244106

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

Dynamics of folded proteins

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Molecular dynamics simulations of biomolecules

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Long-timescale molecular dynamics simulations of protein structure and function.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Atomic-level characterization of the structural dynamics of proteins

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

GPU-accelerated molecular modeling coming of age

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Reversible multiple time scale molecular dynamics

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Design of quasisymplectic propagators for Langevin dynamics.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Efficient treatment of solvation shells in 3D molecular theory of solvation.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Evaluation of the SCF Combination of KS-DFT and 3D-RISM-KH; Solvation Effect on Conformational Equilibria, Tautomerization Energies, and Activation Barriers.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Ab initio study of ionic liquids by KS-DFT/3D-RISM-KH theory

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Helical rosette nanotubes with tunable stability and hierarchy.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

One-pot nucleation, growth, morphogenesis, and passivation of 1.4 nm Au nanoparticles on self-assembled rosette nanotubes

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

3D-RISM-Dock: A New Fragment-Based Drug Design Protocol

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Microtubule stability studied by three-dimensional molecular theory of solvation

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

An MM/3D-RISM approach for ligand binding affinities.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Association thermodynamics and conformational stability of beta-sheet amyloid beta(17-42) oligomers: effects of E22Q (Dutch) mutation and charge neutralization

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Electrolytes in biomolecular systems studied with the 3D-RISM/RISM theory.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Selective ion binding by protein probed with the statistical mechanical integral equation theory.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

A molecular theory of liquid interfaces

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Processed splitting algorithms for rigid-body molecular dynamics simulations.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. I. Microcanonical ensemble.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Overcoming the Barrier on Time Step Size in Multiscale Molecular Dynamics Simulation of Molecular Liquids

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Closed-form expressions of the chemical potential for integral equation closures with certain bridge functions.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Simple electrolyte solutions: comparison of DRISM and molecular dynamics results for alkali halide solutions

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Some Studies Concerning Rotating Axes and Polyatomic Molecules

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Using quaternions to calculate RMSD

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Fast determination of the optimal rotational matrix for macromolecular superpositions

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Optimized Verlet-like algorithms for molecular dynamics simulations.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

The missing term in effective pair potentials

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Solvation Effect on the Conformations of Alanine Dipeptide: Integral Equation Approach

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Integrating diffusion maps with umbrella sampling: application to alanine dipeptide.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

The amino acid dipeptide: small but still influential after 50 years

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Serial Generalized Ensemble Simulations of Biomolecules with Self-Consistent Determination of Weights.

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

1 reference

https://api.crossref.org/works/10.1063%2F1.4848716

21 January 2018

Identifiers

10.1063/1.4848716

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

30 March 2018

http://europepmc.org/abstract/MED/24387356

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q51126779&oldid=1038866883"