Tutorials

In the hands-on afternoon sessions, you will have the option to work on a variety of tutorials. The tutorials recommended for this workshop are listed below. You can find a list of all existing tutorials here, except for Introduction to MD simulations of DNA-protein systems and qwikiMD.

Monday, October 12

Using VMD (listed under VMD Tutorials)
NAMD Tutorial (listed under NAMD Tutorials)
qwikMD (Beta Version available HERE).

Tuesday, October 13

NAMD Tutorial (listed under NAMD Tutorials)
Stretching Deca-Alanine (listed under Free-Energy Methods)
User-Defined Forces in NAMD (listed under NAMD Tutorials)
Introduction to MD simulations of DNA-protein systems

Wednesday, October 14

Parameterizing Small Molecules Using the Force Field Toolkit (listed under Specialized Topics)
Topology File Tutorial (listed under Specialized Topics)

Thursday, October 15

Membrane Proteins Tutorial (listed under Specialized Topics)

Friday, October 16

Alchemical Free Energy Perturbation Calculations (listed under Free-Energy Methods)
Adaptive Biasing Force Calculations (listed under Free-Energy Methods)
Recommended for Advanced Users:
String Method with Swarms of Trajectories (listed under Free-Energy Methods)
Protein:Ligand Standard Binding Free Energies (listed under Free-Energy Methods)