MD - best practices

The aim of this ONLINE course is to give an intro to classical Molecular Dynamics (MD) simulations. We will start from scratch by setting a MD simulation. Regarding the software, we will use 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.

NOTE: The course will be online!

Topics to be covered are:

• Setting up classical MD simulation with NAMD+VMD

Instructor:

Pedro Ojeda

Helper:

Birgitte Brydsö

Initial instructions:

cd /proj/nobackup/projects_folder_name
mkdir username   #or any name you like
cd username
git clone https://github.com/hpc2n/course-md.git 
cd course-md/