Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations

Jana Chocholoušová; Michael Feig

doi:10.1002/jcc.20387

Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.20387 ◽

2006 ◽

Vol 27 (6) ◽

pp. 719-729 ◽

Cited By ~ 64

Author(s):

Jana Chocholoušová ◽

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Surface ◽

Generalized Born ◽

Accurate Representation ◽

Dynamics Simulations

Download Full-text

Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model

Journal of the American Chemical Society ◽

10.1021/ja9939385 ◽

2000 ◽

Vol 122 (11) ◽

pp. 2489-2498 ◽

Cited By ~ 291

Author(s):

Vickie Tsui ◽

David A. Case

Keyword(s):

Molecular Dynamics ◽

Nucleic Acids ◽

Molecular Dynamics Simulations ◽

Solvation Model ◽

Generalized Born ◽

Dynamics Simulations

Download Full-text

Molecular Dynamics Simulations of DNA Using the Generalized Born Solvation Model: Quantitative Comparisons with Explicit Solvation Results

The Journal of Physical Chemistry B ◽

10.1021/jp048757q ◽

2004 ◽

Vol 108 (28) ◽

pp. 10113-10119 ◽

Cited By ~ 14

Author(s):

Zara A. Sands ◽

Charles A. Laughton

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Solvation Model ◽

Generalized Born ◽

Dynamics Simulations ◽

Explicit Solvation

Download Full-text

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

Journal of Computational Chemistry ◽

10.1002/jcc.21813 ◽

2011 ◽

Vol 32 (11) ◽

pp. 2348-2358 ◽

Cited By ~ 15

Author(s):

Yuhang Wang ◽

Jason A. Wallace ◽

Peter H. Koenig ◽

Jana K. Shen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Nonionic Surfactant ◽

Implicit Solvent ◽

Generalized Born ◽

Surfactant Micelles ◽

Implicit Solvent Model ◽

Solvent Model ◽

Dynamics Simulations

Download Full-text

Molecular surface structure of ice(0001): dynamical low-energy electron diffraction, total-energy calculations and molecular dynamics simulations

Surface Science ◽

10.1016/s0039-6028(97)00090-3 ◽

1997 ◽

Vol 381 (2-3) ◽

pp. 190-210 ◽

Cited By ~ 117

Author(s):

N. Materer ◽

U. Starke ◽

A. Barbieri ◽

M.A. Van Hove ◽

G.A. Somorjai ◽

...

Keyword(s):

Molecular Dynamics ◽

Electron Diffraction ◽

Total Energy ◽

Molecular Dynamics Simulations ◽

Surface Structure ◽

Low Energy ◽

Molecular Surface ◽

Low Energy Electron Diffraction ◽

Low Energy Electron ◽

Dynamics Simulations

Download Full-text

Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10470 ◽

2004 ◽

Vol 55 (3) ◽

pp. 620-634 ◽

Cited By ~ 217

Author(s):

Mathew C. Lee ◽

Yong Duan

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Scoring Function ◽

Generalized Born ◽

Amber Force Field ◽

Solvent Model ◽

Dynamics Simulations

Download Full-text

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Journal of Chemical Theory and Computation ◽

10.1021/ct200909j ◽

2012 ◽

Vol 8 (5) ◽

pp. 1542-1555 ◽

Cited By ~ 928

Author(s):

Andreas W. Götz ◽

Mark J. Williamson ◽

Dong Xu ◽

Duncan Poole ◽

Scott Le Grand ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Generalized Born ◽

Dynamics Simulations

Download Full-text

A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations

Journal of Medicinal Chemistry ◽

10.1021/jm030570k ◽

2004 ◽

Vol 47 (12) ◽

pp. 3065-3074 ◽

Cited By ~ 50

Author(s):

Robert C. Rizzo ◽

Samuel Toba ◽

Irwin D. Kuntz

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Basis ◽

Gelatinase A ◽

Generalized Born ◽

Dynamics Simulations

Download Full-text

Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

Download Full-text

Tracer diffusion in perfectly aligned liquid crystalline phases Kinetic theory and molecular dynamics simulations

Molecular Physics ◽

10.1080/00268979709482789 ◽

1997 ◽

Vol 91 (6) ◽

pp. 993-1003 ◽

Cited By ~ 1

Author(s):

ANJALI KHARE ◽

DAVID KOFKE ◽

GLENN EVANS

Keyword(s):

Molecular Dynamics ◽

Kinetic Theory ◽

Molecular Dynamics Simulations ◽

Liquid Crystalline ◽

Tracer Diffusion ◽

Crystalline Phases ◽

Liquid Crystalline Phases ◽

Dynamics Simulations

Download Full-text

ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

Molecular Physics ◽

10.1080/002689798167430 ◽

1998 ◽

Vol 95 (1) ◽

pp. 121-121

Author(s):

CARL MCBRIDE MARK R. WILSON JUDITH A. K.

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulations ◽

Crystal Phases ◽

Dynamics Simulations ◽

Liquid Crystal Phases

Download Full-text