4.7 Article

Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Related references

Note: Only part of the references are listed.
Article Chemistry, Physical

Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats

Cheng Zhang et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Replica Exchange Statistical Temperature Molecular Dynamics Algorithm

Jaegil Kim et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

Article Multidisciplinary Sciences

Folding helical proteins in explicit solvent using dihedral-biased tempering

Cheng Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Article Biochemistry & Molecular Biology

Cooperativity network of Trp-cage miniproteins: probing salt-bridges

Petra Rovo et al.

JOURNAL OF PEPTIDE SCIENCE (2011)

Article Chemistry, Physical

Enhanced sampling and applications in protein folding in explicit solvent

Cheng Zhang et al.

JOURNAL OF CHEMICAL PHYSICS (2010)

Article Chemistry, Physical

Comparison of sampling efficiency between simulated tempering and replica exchange

Cheng Zhang et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

P-LINCS: A parallel linear constraint solver for molecular simulation

Berk Hess

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Physical

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Berk Hess et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Physics, Fluids & Plasmas

Simulation via direct computation of partition functions

Cheng Zhang et al.

PHYSICAL REVIEW E (2007)

Article Chemistry, Physical

Canonical sampling through velocity rescaling

Giovanni Bussi et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Review Chemistry, Physical

Parallel tempering: Theory, applications, and new perspectives

DJ Earl et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2005)

Article Physics, Multidisciplinary

Performance limitations of flat-histogram methods -: art. no. 097201

P Dayal et al.

PHYSICAL REVIEW LETTERS (2004)

Article Chemistry, Multidisciplinary

Smaller and faster:: The 20-residue Trp-cage protein folds in 4 μs

LL Qiu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)

Article Physics, Fluids & Plasmas

Generalization of the Wang-Landau method for off-lattice simulations

MS Shell et al.

PHYSICAL REVIEW E (2002)

Article Biochemistry & Molecular Biology

Designing a 20-residue protein

JW Neidigh et al.

NATURE STRUCTURAL BIOLOGY (2002)