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.
Format: The course will be two half-days and comprises of lectures and hands-on sessions. This is an online-only course (Zoom)
Time: 9:00-12:00 on each day.
Deadline for registration: 2022-03-31
More information, schedule, and registration can be found on the course webpage at HPC2N, Umeå University.