Computational Chemistry - Enhanced Sampling MD Course (NAMD)

This one day MD course will look at Enhanced Sampling Molecular Dynamics, with a focus on NAMD. Two common techniques, i. e. Metadynamics and Accelerated MD, for efficient sampling will be discussed. During the afternoon there will be a hands-on where you get the opportunity to run a NAMD job and get useful tips, from the instructors, for taking advantage of computing resources when running NAMD at HPC2N. 


THIS IS AN OLD COURSE AND EXAMPLE JOB SCRIPTS ARE NO LONGER VALID.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

Please see the main course page for newer, similar courses which may have material available for download.


Topics that will be covered:

  • 10:00 Short Intro to HPC2N, running a batch job
  • 10:30 Molecular Dynamics Simulations
  • 11:30 Enhanced Sampling, Part I (Metadynamics)
  • 12:00 LUNCH BREAK
  • 13:00 Enhanced Sampling, Part II (Accelerated Molecular Dynamics)
  • 14:00 Using NAMD at HPC2N
  • 14:45 COFFEE BREAK
  • 15:00 -16:30 Hands-on (Examples used, as a tar-ball)

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, as well as a basic knowledge of molecular dynamics.

Instructors: Pedro Ojeda May, Birgitte Brydsö

Time and date: 26 February, 2018. 10:00 - 16:30

Location: MIT-Huset, room MC323 (Directions to MIT huset here).

Deadline for registration: 19 February 2018

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

Updated: 2021-09-09, 15:12