Computational Chemistry - MD Simulations (NAMD)

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.

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 THIS IS AN OLD COURSE AND EXAMPLE JOB SCRIPTS ARE NO LONGER VALID.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

Please check the course website for newer courses similar to this one which may have downloadable material.

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

Some example programs for the course can be found i /pfs/nobackup/home/b/bbrydsoe/kebnekaise-intro/ or downloaded as a tar-ball. Some NAMD examples can be found in /home/p/pojedama/Public/waterbox and /home/p/pojedama/Public/protein or they can be downloaded here: protein.tar.gz and waterbox.tar.gz.

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.

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 or the Computational Chemistry - MD Simulations (CHARMM) we held in spring 2017.

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 (Directions to MIT huset here).

Deadline for registration: 14 November 2017.

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