Molecular dynamics simulations in NAMD

It is suggested to participate also in VMD and basic principles in MD theory training sessions. This training course delivered by Dr Karina Kubiak – Ossowska (ARCHIE-WeSt User Support Manager, karina.kubiak@strath.ac.uk) will cover:

1. Running MD simulations in NAMD:

from protein structure to MD simulations
system neutralisation and solvation
minimization, equilibration, heating
the trajectory calculations

2. Advanced MD simulations

Steered MD (SMD)
Particle Mesh Ewald (PME) method