gromacs进阶学习

除了我们常看的gmx manual以外，官网上还有很多信息，多看看对理解gmx有好处，以下我把官网上的信息大致列出来，大家看看有没有感兴趣的专题：

Gromacs 总共分为以下几栏

About Gromacs

Developer Zone //如果要改源码，要读这一部分

Documentation //对gmx有一个深入的了解

Downloads 

GPU acceleration //从4.6版本开始，用了新的gpu架构，里面有测试的参数

Gromacs papers //初始文献

Jobs //招聘

Project ideas //提出的未来的项目

Support //help，里面有举办的培训班信息，比较实用，按专题分类

Documentation

 

• Acceleration and parallelization
• Cut-off schemes
• Errors
• FAQs
• Floating Point Arithmetic
• How-tos
  • Adding a Residue to a Force Field
  • Analysing Trajectory Information
  • Beginners
  • Carbon Nanotube
  • Changing a 3 Point Water Model to a 4 Point Water Model
  • Checkpointing Jobs
  • Constant pH Simulation
  • Diffusion Constant
  • Dihedral PCA
  • Dihedral Restraints
  • Distance Restraints
  • Doing Restarts
  • Essential Dynamics
  • Extending Simulations
  • Free Energy Calculations
  • Plotting Data
  • Build a Linux Cluster
  • Making Disulfide Bonds
  • Membrane Simulations
  • Micelle Clustering
  • Mixed Solvents
  • Multiple Chains
  • Multiple Topology Entries
  • Non-Water Solvation
  • Normal Mode Analysis
  • Parameterization of novel molecules
  • pKa calculations
  • Polymers
  • Position Restraints
  • Potential of Mean Force
  • QMMM
  • Reading XTC From Fortran
  • Reducing Trajectory Storage Volume
  • REMD
  • Removing fastest degrees of freedom
  • Single-Point Energy
  • Speeding Up Simulations
  • Steps to Perform a Simulation
  • Tabulated Potentials
  • Water Solvation
  • Tool Changes for 5.0
  • Trajectory Visualization
  • Using Commands in Scripts
  • Using VMD plugins to read trajectory formats not native to GROMACS
• Include File Mechanism
• Installation Instructions 4.5
  • BlueGene
  • Cmake
  • Compiling QMMM
  • Cygwin
  • GROMACS-OpenMM
  • Intel(R) Cluster Ready Reference
  • Quick and Dirty Installation
  • Windows
• Installation Instructions 4.6
• Installation Instructions 5.0
• Manual
• Performance checklist
• Terminology
  • Average Structure
  • Blowing Up
  • Energy Conservation
  • Constraints and Restraints
  • Molecular Dynamics Simulations
  • Periodic Boundary Conditions
  • Pressure
  • Reproducibility
  • Thermostats
• Tutorials
  • Another Lysozyme Tutorial
  • Free energy of solvation tutorial
  • GROMACS USA Workshop and Conference 2013
    • An introduction to free energy calculations: Michael Shirts, Session 2A
    • An introduction to replica exchange simulations: Mark Abraham, Session 1B
    • Computing potentials of mean force: Justin Lemkul, Session 2A
    • Free energy calculation capabilities in GROMACS: Michael Shirts, Session 1B
    • How long do I need to run my simulations? A guide to thinking about convergence and sampling: Peter Kasson, Session 1B
    • Large-scale automated ensemble simulation with GROMACS & Copernicus: Iman Pouya, Session 2B
    • Membrane Simulations: Justin Lemkul, Session 1A
    • Parallelization schemes and GPU acceleration: Szilard Pall, Session 2B
    • Topology preparation, "What's in a log file", basic performance improvements: Mark Abraham, Session 1A

转载于:https://www.cnblogs.com/qqcwannagraduate/p/4895641.html