Computational Chemistry - MD Simulations (NAMD)

Date: 2017-11-20
Time: 10:00 AM - 4:00 PM
Location: MIT-huset, MA378
The event is for: students - employees

Computational Chemistry - MD Simulations (NAMD)

This one day course is an introduction to Computational Chemistry and MD Simulations, with half of the time dedicated to running NAMD at HPC2N. There will be a hands-on.

Topics that will be covered:

  • 10:00 Short Intro to HPC2N, running a batch job (I)
  • 11:00 Basics on Molecular Dynamics simulations (II):
    • Force Field
    • Ensembles
    • Beyond classical MD simulations: Accelerated MD, Umbrella Sampling, Coarse Graining, Alchemical method
  • 12:00 LUNCH BREAK
  • 13:00 Using NAMD at HPC2N (III)
    • Setting up a simulation
    • Minimization
    • Solvation & Equilibration
    • Production run
    • Some analysis tools
  • 14:30 COFFEE BREAK
  • 14:45 -16:00 Hands-on

Participation is free. Bring your laptop for the hands-on!

The hands-on will be done on HPC2N's systems, so you will need to have an account at HPC2N (or create one when added to the course project) in order to participate in that part.

Lunch and afternoon 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 November 2017, 10:00 - 16:00.

Location: MIT-Huset, room Ma378


Organizer: HPC2N
Contact person: Pedro Ojeda May
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Event type: Workshop
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