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MD simulations with a focus on NAMD

MD simulations with a focus on NAMD

The aim of the course is to let participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files.

We will start from scratch by setting a MD Biomolecular (protein+water) simulation, in the first day of the course. During the second day, we will learn how to setup a steered molecular dynamics simulation (Na-Cl system) and use the results to compute the free energies of separation. Regarding the software, we will use software already installed at HPC2N, i.e. VMD, and NAMD for the full protocol. We will also provide users with a set of best practices to improve the performance of their simulations.

This course will be two half-days. It will have lectures interspersed with live-demo sessions where you get to try out what the instructor shows.

NOTE: The course will be online! We will use Zoom.

Preliminary agenda

Thursday, 2022-04-07

  • 09:00 - 10:10  HPC2N + MD lecture
  • 10:10 - 10:20  Break 
  • 10:20 - 11:10  Exercise: setting up a simulation on the Tk terminal
  • 11:10 - 11:20  Break
  • 11:20 - 12:00  Exercise: setting up a simulation using QwikMD

Friday, 2022-04-08

  • 09:00 - 10:00  SMD/ABF lecture
  • 10:00 - 10:15  Break 
  • 10:15 - 11:00  Exercise: setting up a SMD simulation
  • 11:00 - 11:15  Break
  • 11:15 - 12:00  Exercise: computing free energies
Materials and recording
The presentations and materials can be downloaded here: https://github.com/hpc2n/course-md

The course will be recorded (lectures) and will be seen on HPC2N's YouTube channel.

Audience: This HPC2N course is part of the PRACE Training courses. It is open for academics and people who work in industry in the PRACE member countries. Participation is free. 

The hands-on will be done on HPC2N's systems, so you will need to have an account at HPC2N and at SUPR (or create such accounts) in order to participate in that part.

Course project: As part of the hands-on, you will be given temporary access to a course project, which will be used for running the hands-on examples. There are some policies regarding this, that we ask that you follow:

  • You may be given access to the project before the course; please do not use the allocation for running your own codes in. Usage of the project before the course means the priority of jobs submitted to it goes down, diminishing the opportunity for you and your fellow participants to run the examples during the course. You can read more detailed information about the job policies at HPC2N here.
  • The course project will be open 1-2 weeks after the course, giving the participants the opportunity to test run examples and shorter codes related to the course. During this time, we ask that you only use it for running course related jobs. Use your own discretion, but it could be: (modified) examples from the hands-on, short personal codes that have been modified to test things learned at the course, etc.
  • Anyone found to be misusing the course project, using up large amounts of the allocation for their own production runs, will be removed from the course project.

The course uses computing resources provided by the Swedish National Infrastructure for Computing (SNIC) at HPC2N partially funded by the Swedish Research Council through grant agreement no. 2018-05973.


Instructor: Pedro Ojeda May

Helper: Birgitte Brydsö

Time and date: 7-8 April, 2022, 9:00 - 12:00 each day.

Location: ONLINE

Deadline for registration: 31 March 2022.

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

Updated: 2024-06-25, 16:43