Visualization in VMD

This training session is dedicated mainly for people running Molecular Dynamics simulations, nevertheless it is possible to use VMD for other purposes.  This training delivered by Dr Karina Kubiak – Ossowska (ARCHIE-WeSt User Support Officer, karina.kubiak [at] strath [dot] ac [dot] uk) will cover:

  • loading the file (molecule) and information file (psf file, trajectory file)
  • display methods
  • graphical representations, selections
  • labelling, changing the font
  • making a nice figure and movie
  • using tcl scripts
  • structure analysis
  • modelling using VMD (adding ions, solvatation)