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