计算模拟的软件包, 分析程序和常用库 (随手更新, 也是给自己的备忘)

• Basic methods, tutorial code
  Allen-Tildesley code (Fortran and Python)

• Markov State Model (MSM):
  PyEMMA
  现在的网址是: http://www.emma-project.org
  2019.5 pyemma new tutorial example
  (if can not install mdshare, go to http://ftp.imp.fu-berlin.de/pub/cmb-data/ for tutorial data.)

  MSMBuilder
  现在的网址是: http://msmbuilder.org

  (补充:
  SimTk是一个好网站, 从上面可以找到大量正在开发的面向模拟的软件, 可以一淘. 软件是否好用就得试一试了.)

  MSM相关, 好用的包(python):
  PyEMMA, msmtools, ...
  msmtools (low-level interface to basic algorithms, 适合自己调用)
  PyEMMA (high-level interface to MSM functionalities)

• Path sampling (python, 2016 开始在github上开发)
  或者官网:
  http://openpathsampling.org
  官网包含一些适合初学者的例子, 比如:
  flexible length TPS on Alanine Dipeptide
  非常值得一试\(^o^)/
  (开发者是: Jan-Hendrik Prinz, David W.H. Swenson, John Chodera, Peter Bolhuis)

• Lammps
  Lammps是一个功能强大的模拟程序包.
  最近发现一个相关的非常好的模拟论坛, 还带了知乎专栏和微信公众号.
  一定要学一下这个软件包, 至少在模拟multichain homopolymers很有用, 可以MD+lammps自带的bond bridging算法.

• 其它有趣的东西:
  pywonderland(包含代码, 从py脚本生成精美的图片. 可以学习PIL以及一些其它的Python包, 还有POV-RAY的python相关包的应用例子)

  Reaction-diffusion systems

• Event-driven simulation
  DynamO
  DynamO also supports several advanced algorithms for accelerated dynamics: parallel tempering/replica exchange, histogram reweighting, multicanonical simulations.

• Gromacs Amber 良心博客
  Jerkwin 国内
  Jerkwin github
  Jerkwin 评论

Jerkwin 使用antechamber和GAFF模拟药物分子

Jerkwin GROMACS非标准残基教程1：修改力场与增加残基

Jerkwin 分子动力学, 红外光谱 1
Jerkwin 分子动力学, 红外光谱 2

• NAMD metadynamics

Brief intro to Metadynamics with NAMD

• 1D/2D Umbrella sampling + WHAM, Amber MD trajectories, MDToolbox (Octave/MATLAB files) http://mdtoolbox.readthedocs.io/en/latest/introduction.html
  Docker image for MDToolbox
  Normal mode analysis of ANM

• VASP
  发现有一个不错的入门教程, 分为许多小结, 值得看看: Learn VASP The Hard Way

• Hamiltonian Monte Carlo | Hybrid Monte Carlo
  MCMC: Hamiltonian Monte Carlo (a.k.a. Hybrid Monte Carlo)

• Enhanced sampling methods

• Wang-Landau sampling
  REWL (REWL + MPI (2017 paper and code) )
  GPU
  REWL + GPU (REWL + CUDA Fortran (2018 Potts model paper and sample block code in the paper) )

• Multicanonical sampling
  GPU (MUCA + CUDA (paper and code) )

• Enhanced sampling software toolkits
  FEASST (Free Energy and Advanced Sampling Simulation Toolkit) (strongly recommend)

• Allen 书 Computer simulation of liquids (2017, 2ed) 特别棒, 就需要这本书! 书中有WL, REMC, DPD等等内容以及相关代码(github下载, 有fortran90版和python版), 简直要感动哭了. 找空余时间仔细看看这本书加的新内容和代码.

• PSCF