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 [at] strath [dot] ac [dot] 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