From wiki.gromacs.org

[edit] Welcome

This is the wiki dealing with GROMACS (http://www.gromacs.org), a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Feature summary lists some of the key features of GROMACS that make it stand out from the competition.

[edit] GROMACS-Specific Information

[edit] Getting Started

• GROMACS Website - should be the first port of call.
• GROMACS Feature Summary
• Installation - procedures required to install the GROMACS software package and some issues that may arise.
• Beginners - for those starting out with molecular dynamic simulations or GROMACS.
• Test-set - information about how you can test your GROMACS installation

[edit] Usage

• GROMACS Utilities - descriptions and links to man pages for programs provided with the GROMACS software package.
• GROMACS File Types - file formats used and generated by the GROMACS utilities.
• Tools - non-GROMACS scripts, software, utilities and tools for performing and analysing simulations.

• Tutorials - best way to learn something is by doing yourself, these assist in the learning process with providing step by step instructions.
• HOWTOs - how to instructions on performing a number of processes.

• Force Fields - these are what defines the parameters detailing how particles interact with each other in a simulation.
• Best Practices - things that you should do and avoid doing, when simulating.

[edit] Workshops

• Stanford 2008 Workhop - Material from the April 2008 workshop on free energy and other advanced methods.

[edit] Development

Information about GROMACS development is concentrated on the Development page. The information includes coding standards, accessing the development code from CVS. There also is a list of major and minor Development projects that we would like some people outside the core developers to work on. The topics include hardcore programming, but also making tutorials and helping out with websites.

[edit] General

• Articles About GROMACS - published journal articles about the GROMACS package itself.
• Articles That Used GROMACS - published journal articles in which the authors utilised the GROMACS package.

[edit] Help

• FAQs - frequently asked questions covering all areas.
• Errors - information and solutions for some errors that can be encountered while using GROMACS.
• Support - where to get help / assistance when can't find it for yourself.
• GROMACS Bugzilla - report, confirm, and track bugs related to the GROMACS package.

[edit] General Information

• Molecular Dynamics Simulations - Links to introductory books, videos, web sites.
• Statistical Mechanics - Links to general information sites: stuff that you should know
• Linux Cluster - How to roll your own