Results 1 - 10 of 31

Development and testing of a general amber force field.

by Junmei Wang , Romain M Wolf , James W Caldwell , Peter A Kollman , David A Case - J Comput Chem;25:1157–1174. , 2004
"... Abstract: We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogen ..."
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Abstract: We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

by Alexey Savelyev, Er D. Mackerell
"... ABSTRACT: Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for ba ..."
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ABSTRACT: Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure

2014. AMBER-DYES: characterization of charge fluctuations and force field parametrization of fluorescent dyes for molecular dynamics simulations

by Timo Graen, Martin Hoefling
"... ABSTRACT: Recent advances in single molecule fluores-cence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomo ..."
Abstract - Cited by 1 (0 self) - Add to MetaCart
ABSTRACT: Recent advances in single molecule fluores-cence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing

An improved empirical potential energy function for molecular simulations of phospholipids

by Scott E. Feller, Alexander D. Mackerell - J. Phys. Chem. B
"... Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) hydrocarbon and torsional parameters and to the partial atomic charges and torsional parameters of the phosphate moiety. The ..."
Abstract - Cited by 34 (1 self) - Add to MetaCart
bilayer. Of note is the influence of the hydrocarbon LJ parameters on the conformational properties of the aliphatic tails, emphasizing the importance of obtaining the proper balance between the bonded and nonbonded portions of the force field. Compatibility with the CHARMM all-atom parameter sets

GROMACS Molecule & Liquid Database

by David Van Der Spoel, Paul J. Van Maaren, Carl Caleman
"... Motivation: The molecular dynamics simulation package GROMACS (Hess et al., 2008) is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, ..."
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, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations it is necessary to compare results from the simulations to experimental data. To ease the process of setting up

Databases and ontologies Advance Access publication January 11, 2012 GROMACS molecule & liquid database

by David Van Der Spoel, Paul J. Van Maaren, Carl Caleman, Jonathan Wren , 2011
"... Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with ..."
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Motivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible

134 PUBLICATIONS 2,844 CITATIONS SEE PROFILE

by Aurélien Grosdidier, Vincent Zoete, Olivier Michielin, Vincent Zoete, Olivier Michielin
"... Abstract: The prediction of binding modes (BMs) occurring between a small molecule and a target protein of bio-logical interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. Nowadays, the univ ..."
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Abstract: The prediction of binding modes (BMs) occurring between a small molecule and a target protein of bio-logical interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. Nowadays

unknown title

by Harvey R. Brown, Oliver Pooley , 1999
"... The origin of the spacetime metric: Bell’s ‘Lorentzian pedagogy ’ and its significance in general relativity ∗ ..."
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The origin of the spacetime metric: Bell’s ‘Lorentzian pedagogy ’ and its significance in general relativity ∗

unknown title

by Harvey R. Brown, Oliver Pooley , 1999
"... The origin of the spacetime metric: Bell’s ‘Lorentzian pedagogy ’ and its significance in general relativity ∗ ..."
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The origin of the spacetime metric: Bell’s ‘Lorentzian pedagogy ’ and its significance in general relativity ∗

unknown title

by A. Szameit, Y. Shechtman, H. Dana, S. Steiner, S. Gazit, E. Bullkich, O. Cohen, Y. C. Eldar, S. Shoham, E. B. Kley, M. Segev
"... We present the experimental reconstruction of sub-wavelength features from the far-field of sparse optical objects. We show that it is sufficient to know that the object is sparse, and only that, and recover 100 nm features with the resolution of 30 nm, for an illuminating wavelength of =532 nm. Our ..."
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We present the experimental reconstruction of sub-wavelength features from the far-field of sparse optical objects. We show that it is sufficient to know that the object is sparse, and only that, and recover 100 nm features with the resolution of 30 nm, for an illuminating wavelength of =532 nm
Results 1 - 10 of 31