Course: Computational Chemistry - MD Simulations, 2016-06-20

Computational Chemistry - MD Simulations

This one day course is an introduction to Computational Chemistry and MD Simulations, with half of the time dedicated to running GROMACS at HPC2N. There will be a hands-on. Bring your own protein/system if you have it, and want help with running it.

Topics that will be covered:

• 08:30 Basics on Molecular Dynamics simulations:
  • Force Field
  • Ensembles
  • Beyond classical MD simulations: Accelerated MD, Umbrella Sampling, Coarse Graining, Alchemical method
• 10:30 COFFEE BREAK
• 11:00 Abisko intro + Brief talk about the new cluster
• 11:45 LUNCH BREAK
• 12:45 Using GROMACS at HPC2N
  • Setting up a simulation
  • Minimization
  • Solvation & Equilibration
  • Production run
  • Some analysis tools
• 14:30 COFFEE BREAK
• 14:45 Using GROMACS/Visualization tools (VMD) at HPC2N
• 15:15  - 16:30  Hands-on

Participation is free.

Slides from the presentation: Comp. Chem. [PDF] | HPC2N intro [PDF]

Examples from the hands-on: Classical [tar] | Nanotubes [tar]

NOTE: THIS IS AN OLD COURSE AND EXAMPLE JOB SCRIPTS ARE NO LONGER VALID. THUS, THE MATERIAL IS NO LONGER AVAILABLE FOR DOWNLOAD!

Lunch and coffee will be provided.

Prerequisites: The participants are expected to have a basic knowledge of programming.

Instructors: Pedro Ojeda May, Birgitte Brydsö

Time and date: 20. June 2016, 08:30 - 16:30

Location: MIT-Huset, room MC313 (Directions to MIT huset here).

Deadline for registration: 13. June 2016.

Please register using this form. All fields are mandatory. Registration closed. Please contact Pedro Ojeda May to ask if you can join the course.