MD simulations with a focus on NAMD (HPC2N, UmU), 2022-04-(07-08)

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Name MD simulations with a focus on NAMD (HPC2N, UmU), 2022-04-(07-08)
Description MD simulations with a focus on NAMD
Type of event Course
Location Umeå
Start date 2022-04-07
End date 2022-04-08

Course overview

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.

The course will be completely online. We will use Zoom.

Course web page and registration

For more information and registration refer to the course webpage