(Q30453963)

21 June 2017

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase (English)

1 reference

21 June 2017

2

Michael R Shirts

1 reference

21 June 2017

Tri T Pham

1

1 reference

PubMed ID

21786994

21 June 2017

language of work or name

English

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publication date

1 July 2011

1 reference

Journal of Chemical Physics

21 June 2017

1 reference

21 June 2017

135

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21 June 2017

3

1 reference

21 June 2017

034114

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Computations of standard binding free energies with molecular dynamics simulations

21 June 2017

1 reference

Hit identification and binding mode predictions by rigorous free energy simulations

21 January 2018

1 reference

Basic ingredients of free energy calculations: a review

21 January 2018

1 reference

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

21 January 2018

1 reference

Integration of virtual and high-throughput screening

21 January 2018

1 reference

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

21 January 2018

1 reference

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Statistically optimal analysis of samples from multiple equilibrium states

21 January 2018

1 reference

Replica-exchange method using the generalized effective potential.

21 January 2018

1 reference

Efficient sampling of protein structures by model hopping.

21 January 2018

1 reference

Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

21 January 2018

1 reference

Replica exchange with solute tempering: efficiency in large scale systems

21 January 2018

1 reference

Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

21 January 2018

1 reference

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

21 January 2018

1 reference

Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions.

21 January 2018

1 reference

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

21 January 2018

1 reference

Variance minimization of free energy estimates from optimized expanded ensembles

21 January 2018

1 reference

Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions.

21 January 2018

1 reference

Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS).

21 January 2018

1 reference

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

21 January 2018

1 reference

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

21 January 2018

1 reference

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

21 January 2018

1 reference

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

21 January 2018

1 reference

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

Free energy via molecular simulation: applications to chemical and biomolecular systems

21 January 2018

1 reference

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

1 reference

Multidimensional replica-exchange method for free-energy calculations

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.3607597

1 reference

21 June 2017

1 reference

PubMed ID

21786994