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 (Knowledge Exchange Associate, ARCHIE-WeSt, 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