Molecular dynamics simulations in NAMD

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