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Computational Chemistry - MD Simulations (CHARMM)

Computational Chemistry - MD Simulations (CHARMM)

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

Topics that will be covered (links goes to slides used in that section of the course):

  • 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 CHARMM 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

Small batch examples [tar.gz].

Small CHARMM example [tar.gz].

(About both above: Any instances of proj. id. should be changed to your own proj. id. after the course).


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 ARE NO LONGER VALID.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

Check the course website for newer courses which may have material available.


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).

Lunch and afternoon coffee will be provided.

Note that you do not need to participate in parts (I) and (II) of the schedule if you already did those for the Computational Chemistry - MD / Gromacs course we held in 2016.

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

Instructors: Pedro Ojeda May, Birgitte Brydsö

Time and date: 04. May 2017, 10:00 - 16:00.

Location: MIT-Huset, room MA166 (Directions to MIT huset here).

Deadline for registration: 27. April 2017.

Please register using this form. All fields marked with * are mandatory. REGISTRATION CLOSED!

Updated: 2021-09-09, 15:12