Results 221 to 230 of about 161,635 (280)

Development and testing of a general amber force field

Journal of Computational Chemistry, 2004
Junmei Wang, Romain M Wolf, David A Case
exaly   +2 more sources

Lipid21: Complex Lipid Membrane Simulations with AMBER

Journal of Chemical Theory and Computation, 2022
We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains.
Callum J Dickson, Ian Gould
exaly   +2 more sources

The Amber biomolecular simulation programs

Journal of Computational Chemistry, 2005
David A Case, Thomas E Cheatham, Holger Gohlke   +2 more
exaly   +2 more sources

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

Proteins: Structure, Function and Bioinformatics, 2010
Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these ...
Kresten Lindorff-Larsen, Stefano Piana, David E Shaw   +2 more
exaly   +2 more sources

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

Proteins: Structure, Function and Bioinformatics, 2006
Asim Okur, Carlos L Simmerling
exaly   +2 more sources

A fast and high-quality charge model for the next generation general AMBER force field

Journal of Chemical Physics, 2020
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the world to perform in silico simulations and modelings on diverse scientific topics, especially in the field of computer-aided drug design whose primary task is to ...
Xibing He, Man Hoang Viet, Wei Yang
exaly   +2 more sources

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An overview of the Amber biomolecular simulation package

Wiley Interdisciplinary Reviews: Computational Molecular Science, 2013
David A Case
exaly   +2 more sources

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

Journal of Chemical Theory and Computation, 2013
Andreas W Götz
exaly   +2 more sources

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

Journal of Chemical Theory and Computation, 2012
We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs).
Andreas W Götz, Mark J Williamson, Dong Xu   +2 more
exaly   +2 more sources