(Q51608239)

8 April 2018

title

Velocity scaling for optimizing replica exchange molecular dynamics. (English)

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author name string

Maksim Kouza

series ordinal

1

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Ulrich H E Hansmann

series ordinal

2

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language of work or name

English

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publication date

1 January 2011

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8 April 2018

Journal of Chemical Physics

published in

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volume

134

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issue

4

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page(s)

044124

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Generalized ensemble and tempering simulations: a unified view.

cites work

1 reference

Folding proteins by first-passage-times-optimized replica exchange

21 January 2018

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Understanding protein folding: small proteins in silico

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Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk

21 January 2018

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Thermostat artifacts in replica exchange molecular dynamics simulations

21 January 2018

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Generalized replica exchange method

21 January 2018

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Exchange Often and Properly in Replica Exchange Molecular Dynamics

21 January 2018

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A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

21 January 2018

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

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21 January 2018

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21 January 2018

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All-Atom Structure Prediction and Folding Simulations of a Stable Protein

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Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

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Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

21 January 2018

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

21 January 2018

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

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Comparison of simple potential functions for simulating liquid water

21 January 2018

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Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

21 January 2018

1 reference

Folding of the protein domain hbSBD

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

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

21 January 2018

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Effect of finite size on cooperativity and rates of protein folding.

21 January 2018

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Dependence of protein mechanical unfolding pathways on pulling speeds.

21 January 2018

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New force replica exchange method and protein folding pathways probed by force-clamp technique.

21 January 2018

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Molecular Dynamics Approach to Aggregation of Polymer Chains with Monomers Connected by Rigid Bonds

21 January 2018

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Molecular Dynamics Approach to Aggregation of Polymer Chains with Monomers Connected by Springs

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.3533236

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8 April 2018

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8 April 2018