Updating conversion, creating readmes
This commit is contained in:
Jonas Zeunert
@@ -4,7 +4,7 @@
|
||||
[38;5;12m [39m
|
||||
|
||||
|
||||
[38;5;12m [39m[38;2;255;187;0m[1m[4mAwesome Molecular Dynamics [0m
|
||||
[38;5;12m [39m[38;2;255;187;0m[1m[4mAwesome Molecular Dynamics [0m
|
||||
[38;5;14m[1m![0m[38;5;12mAwesome[39m[38;5;14m[1m [0m[38;5;14m[1m(https://awesome.re/badge.svg)[0m[38;5;12m [39m[38;5;12m(https://awesome.re)[39m[38;5;12m [39m[38;5;14m[1m![0m[38;5;12mGitHub[39m[38;5;12m [39m[38;5;12mstars[39m[38;5;14m[1m [0m[38;5;14m[1m(https://img.shields.io/github/stars/ipudu/awesome-molecular-dynamics.svg?style=social&label=Stars)[0m[38;5;12m [39m
|
||||
[38;5;12m(https://github.com/ipudu/awesome-molecular-dynamics/stargazers)[39m[38;5;12m [39m[38;5;14m[1m![0m[38;5;12mSay[39m[38;5;12m [39m[38;5;12mThanks![39m[38;5;14m[1m [0m[38;5;14m[1m(https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)[0m[38;5;12m [39m[38;5;12m(https://saythanks.io/to/ipudu)[39m
|
||||
|
||||
@@ -27,11 +27,9 @@
|
||||
|
||||
[38;2;255;187;0m[4mBooks[0m
|
||||
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mComputer[0m[38;5;14m[1m [0m[38;5;14m[1mSimulation[0m[38;5;14m[1m [0m[38;5;14m[1mof[0m[38;5;14m[1m [0m[38;5;14m[1mLiquids[0m[38;5;12m [39m[38;5;12m(https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mA[39m[38;5;12m [39m[38;5;12mclassic[39m[38;5;12m [39m[38;5;12mbook[39m[38;5;12m [39m[38;5;12mon[39m[38;5;12m [39m[38;5;12mmolecular[39m[38;5;12m [39m[38;5;12mdynamics[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mMonte[39m[38;5;12m [39m[38;5;12mCarlo[39m[38;5;12m [39m[38;5;12msimulations[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mliquids.[39m[38;5;12m [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m
|
||||
[38;5;14m[1mcsol-code[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mComputer Simulation of Liquids[0m[38;5;12m (https://www.amazon.com/Computer-Simulation-Liquids-Michael-Allen/dp/0198803206) - A classic book on molecular dynamics and Monte Carlo simulations of liquids. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mcsol-code[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mUnderstanding[0m[38;5;14m[1m [0m[38;5;14m[1mMolecular[0m[38;5;14m[1m [0m[38;5;14m[1mSimulation:[0m[38;5;14m[1m [0m[38;5;14m[1mFrom[0m[38;5;14m[1m [0m[38;5;14m[1mAlgorithms[0m[38;5;14m[1m [0m[38;5;14m[1mto[0m[38;5;14m[1m [0m[38;5;14m[1mApplications[0m[38;5;12m [39m
|
||||
[38;5;12m(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)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mMolecular[39m[38;5;12m [39m[38;5;12msimulation[39m[38;5;12m [39m[38;5;12mbible.[39m[38;5;12m [39m
|
||||
[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mums-code[0m[38;5;12m [39m
|
||||
[38;5;12m(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)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mMolecular[39m[38;5;12m [39m[38;5;12msimulation[39m[38;5;12m [39m[38;5;12mbible.[39m[38;5;12m [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mums-code[0m[38;5;12m [39m
|
||||
|
||||
[38;5;14m[1mcsol-code[0m[38;5;12m : https://github.com/Allen-Tildesley/examples[39m
|
||||
[38;5;14m[1mums-code[0m[38;5;12m : http://www.acmm.nl/molsim/frenkel_smit/README.html[39m
|
||||
@@ -44,8 +42,7 @@
|
||||
[38;2;255;187;0m[4mMD Engines/Frameworks[0m
|
||||
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAmber[0m[38;5;12m (http://ambermd.org/) - A suite of biomolecular simulation programs. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mamber-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mASE[0m[38;5;12m [39m[38;5;12m(https://wiki.fysik.dtu.dk/ase/)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mThe[39m[38;5;12m [39m[38;5;12mAtomic[39m[38;5;12m [39m[38;5;12mSimulation[39m[38;5;12m [39m[38;5;12mEnvironment[39m[38;5;12m [39m[38;5;12m(ASE)[39m[38;5;12m [39m[38;5;12mis[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mset[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mtools[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mPython[39m[38;5;12m [39m[38;5;12mmodules[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12msetting[39m[38;5;12m [39m[38;5;12mup,[39m[38;5;12m [39m[38;5;12mmanipulating,[39m[38;5;12m [39m[38;5;12mrunning,[39m[38;5;12m [39m[38;5;12mvisualizing[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12manalyzing[39m[38;5;12m [39m[38;5;12matomistic[39m[38;5;12m [39m[38;5;12msimulations.[39m[38;5;12m [39m
|
||||
[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mase-code[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mASE[0m[38;5;12m (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. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mase-code[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCHARMM[0m[38;5;12m (https://www.charmm.org/) - A molecular simulation program with broad application to many-particle systems. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mcharmm-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mGromacs[0m[38;5;12m (http://www.gromacs.org/) - A molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mgromacs-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mgromacs-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mHOOMD-Blue[0m[38;5;12m (http://glotzerlab.engin.umich.edu/hoomd-blue/) - A general-purpose, python-based, GPU-accelerated molecular dynamics and Monte Carlo simulation framework. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mhoomd-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mhoomd-doc[0m[38;5;12m [39m
|
||||
@@ -85,8 +82,8 @@
|
||||
|
||||
[38;2;255;187;0m[4mVisualization Tools[0m
|
||||
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAvogadro[0m[38;5;12m [39m[38;5;12m(https://avogadro.cc/)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mAn[39m[38;5;12m [39m[38;5;12madvanced[39m[38;5;12m [39m[38;5;12mmolecule[39m[38;5;12m [39m[38;5;12meditor[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mvisualizer[39m[38;5;12m [39m[38;5;12mdesigned[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mcross-platform[39m[38;5;12m [39m[38;5;12muse[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mcomputational[39m[38;5;12m [39m[38;5;12mchemistry,[39m[38;5;12m [39m[38;5;12mmolecular[39m[38;5;12m [39m[38;5;12mmodeling,[39m[38;5;12m [39m[38;5;12mbioinformatics,[39m[38;5;12m [39m[38;5;12mmaterials[39m[38;5;12m [39m[38;5;12mscience,[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mrelated[39m[38;5;12m [39m
|
||||
[38;5;12mareas.[39m[38;5;12m [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mavogadro-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mavogadro-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAvogadro[0m[38;5;12m [39m[38;5;12m(https://avogadro.cc/)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mAn[39m[38;5;12m [39m[38;5;12madvanced[39m[38;5;12m [39m[38;5;12mmolecule[39m[38;5;12m [39m[38;5;12meditor[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mvisualizer[39m[38;5;12m [39m[38;5;12mdesigned[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mcross-platform[39m[38;5;12m [39m[38;5;12muse[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mcomputational[39m[38;5;12m [39m[38;5;12mchemistry,[39m[38;5;12m [39m[38;5;12mmolecular[39m[38;5;12m [39m[38;5;12mmodeling,[39m[38;5;12m [39m[38;5;12mbioinformatics,[39m[38;5;12m [39m[38;5;12mmaterials[39m[38;5;12m [39m[38;5;12mscience,[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mrelated[39m[38;5;12m [39m[38;5;12mareas.[39m[38;5;12m [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mavogadro-code[0m
|
||||
[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mavogadro-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mVMD[0m[38;5;12m (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. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mvmd-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPlato[0m[38;5;12m (https://plato-draw.readthedocs.io/) - A python library for both interactive and figure-grade visualizations of particle systems. [39m[38;5;14m[1m:octocat:[0m[38;5;12m [39m[38;5;14m[1mplato-code[0m[38;5;12m [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mplato-doc[0m[38;5;12m [39m
|
||||
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPyMOL[0m[38;5;12m (https://pymol.org/2/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. [39m[38;5;14m[1m:book:[0m[38;5;12m [39m[38;5;14m[1mpymol-doc[0m[38;5;12m [39m
|
||||
|
||||
Reference in New Issue
Block a user