Department of Biochemistry, Virginia Tech
|Tutorial 1: Lysozyme in Water||Tutorial 2: KALP15 in DPPC||Tutorial 3: Umbrella Sampling|
|Tutorial 4: Biphasic Systems||Tutorial 5: Protein-Ligand Complex||Tutorial 6: Free Energy Calculations|
|Tutorial 7: Virtual Sites|
These tutorials are designed as introductory material into using the GROMACS simulation package. GROMACS is open-source software, and has consistently been one of the fastest (if not the fastest) molecular dynamics codes available.
There are currently six tutorials available:
Various other tutorials are in development and will be posted as they are ready.
Most of these tutorials assume you are using version 4.5.3 of GROMACS or newer. If you are using an older version, not all of the features detailed here will work! Some of the .mdp options and command line arguments change substantially between versions. Each tutorial states which version it expects you are using. If you are using a different version, be forewarned: the tutorials likely will not work as expected.
At the end of each tutorial you will find my contact information in order to provide commentary or report anything you find to be incorrect. I genuinely appreciate this kind of feedback, as it helps me design better tutorials and fix things that are not clear (or sometimes wrong, oops). I must ask that you do not contact me for general GROMACS help, advice on your project, or any other purpose. I provide these tutorials as a service to the GROMACS community, without warranty or guarantee of technical support. I am continually inundated with help requests and I simply do not have the time to be helpful to everyone. I already deal with enough email :)
I hope you find these tutorials useful. Enjoy.
For GROMACS installation instructions, refer here.
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