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Jonas Zeunert
2024-04-23 15:17:38 +02:00
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 Awesome Molecular Dynamics 
 Awesome Molecular Dynamics 
!Awesome (https://awesome.re/badge.svg) (https://awesome.re) !GitHub stars (https://img.shields.io/github/stars/ipudu/awesome-molecular-dynamics.svg?style=social&label=Stars) 
(https://github.com/ipudu/awesome-molecular-dynamics/stargazers) !Say Thanks! (https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg) (https://saythanks.io/to/ipudu)
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Books
⟡ Computer Simulation of Liquids (https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206) - A classic book on molecular dynamics and Monte Carlo simulations of 
liquids. :octocat: csol-code 
⟡ Computer Simulation of Liquids (https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206) - A classic book on molecular dynamics and Monte Carlo simulations of liquids. :octocat: csol-code 
⟡ Understanding Molecular Simulation: From Algorithms to Applications 
(https://www.amazon.com/Understanding-Molecular-Simulation-Second-Computational/dp/0122673514/ref=sr_1_1?ie=UTF8&qid=1530897897&sr=8-1&keywords=understanding+molecular+simulation) - Molecular
simulation bible. :octocat: ums-code 
(https://www.amazon.com/Understanding-Molecular-Simulation-Second-Computational/dp/0122673514/ref=sr_1_1?ie=UTF8&qid=1530897897&sr=8-1&keywords=understanding+molecular+simulation) - Molecular simulation bible. :octocat: ums-code 
csol-code : https://github.com/Allen-Tildesley/examples
ums-code : http://www.acmm.nl/molsim/frenkel_smit/README.html
@@ -44,19 +42,15 @@
MD Engines/Frameworks
⟡ Amber (http://ambermd.org/) - A suite of biomolecular simulation programs. :book: amber-doc 
⟡ ASE (https://wiki.fysik.dtu.dk/ase/) - The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing 
atomistic simulations. :octocat: ase-code 
⟡ ASE (https://wiki.fysik.dtu.dk/ase/) - The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. :octocat: ase-code 
⟡ CHARMM (https://www.charmm.org/) - A molecular simulation program with broad application to many-particle systems. :book: charmm-doc 
⟡ Gromacs (http://www.gromacs.org/) - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. :octocat: gromacs-code :book: gromacs-doc 
⟡ HOOMD-Blue (http://glotzerlab.engin.umich.edu/hoomd-blue/) - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. :octocat: hoomd-code 
:book: hoomd-doc 
⟡ HOOMD-Blue (http://glotzerlab.engin.umich.edu/hoomd-blue/) - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. :octocat: hoomd-code :book: hoomd-doc 
⟡ ipi (http://ipi-code.org) - i-PI: a universal force engine. :octocat: ipi-code 
⟡ LAMMPS (http://lammps.sandia.gov/) - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. :octocat: lammps-code :book: 
lammps-doc 
⟡ LAMMPS (http://lammps.sandia.gov/) - A classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. :octocat: lammps-code :book: lammps-doc 
⟡ OpenMM (http://openmm.org/) - A toolkit for molecular simulation using high performance GPU code. :octocat: openmm-code :book: openmm-doc 
⟡ pyiron (http://pyiron.org) - pyiron - an integrated development environment (IDE) for computational materials science. :octocat: pyiron-code 
⟡ Tinker (https://dasher.wustl.edu/tinker/) - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. :octocat: tinker-code :book: 
tinker-doc 
⟡ Tinker (https://dasher.wustl.edu/tinker/) - A complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. :octocat: tinker-code :book: tinker-doc 
amber-doc : http://ambermd.org/doc12/Amber16.pdf
ase-code : https://gitlab.com/ase/ase
@@ -88,10 +82,9 @@
Visualization Tools
⟡ Avogadro (https://avogadro.cc/) - An advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials 
science, and related areas. :octocat: avogadro-code :book: avogadro-doc 
⟡ VMD (http://www.ks.uiuc.edu/Research/vmd/) - A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
:book: vmd-doc 
⟡ Avogadro (https://avogadro.cc/) - An advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. :octocat: avogadro-code
:book: avogadro-doc 
⟡ VMD (http://www.ks.uiuc.edu/Research/vmd/) - A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. :book: vmd-doc 
⟡ Plato (https://plato-draw.readthedocs.io/) - A python library for both interactive and figure-grade visualizations of particle systems. :octocat: plato-code :book: plato-doc 
⟡ PyMOL (https://pymol.org/2/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. :book: pymol-doc 
⟡ OVITO (https://ovito.org/) - OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. :book: ovito-doc