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