Molecular Dynamics Flexible Fitting
Documentation
MDFF and xMDFF tutorial (html)
(pdf,
3.0M)
(required tutorial files [.tar.gz, 195M] [.zip, 195M], individual files)
The MDFF tutorial includes sections on MDFF in vacuum and with explicit solvent, with domain restraints, with symmetry restraints, xMDFF, the MDFF GUI (and interactive MDFF), and Timeline
analysis.
QwikMD / MDFF GUI.
(individual tutorial files)
How to perform MDFF of Adenylate Kinase using QwikMD to easily set up the simulation.
Structure Check tutorial
(html)
(pdf,
720K)
(required tutorial files [.tar.gz, 762K] [.zip, 753K], individual files)
This tutorial described VMD plugins that can be used to identify, visualize, fix, and prevent certain structure errors (read more).
Rosetta/MDFF (html)
(pdf,
2.7M)
(required tutorial files [.tar.gz, 221M] [.zip, 221M], individual files)
Interactive Model Building with Rosetta and MDFF.
VMD mdff plugin documentation (html) Documentation page containing usage information for the mdff plugin and MDFF GUI in VMD.
For other VMD and NAMD tutorials, click here.
