Protein Simulation

Hands on introduction to protein simulation using VMD and NAMD.

The data files correspond to an example simulation of the human ubiquitin protein (PDB code: 1UBQ) generated from experimental data.

Important:

• The instructions for the preparation and execution of the simulation ara available here.
• Sample scripts and forcefield files for executing and analyzing NAMD simulations are available here: https://github.com/jfaraudo/Running_NAMD

Notes:

• This example is related (but not equal) to the official NAMD tutorial.
• It is also similar to the example tutorial recently proposed for GROMACS in the context of BioExcel tutorials.