QM/MM - best practices

The aim of this ONLINE course is to give an intro to classical Molecular Dynamics (MD) simulations and the combined Quantum Mechanical and Molecular Mechanics (QM/MM) simulations. We will start from scratch by setting a MD simulation, in the first half-day of the course, and then use this system to setup a QM/MM simulation. Regarding the software, we will use VMD, NAMD, ORCA, and GAUSSIAN for the full QM/MM 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 and QM/MM simulations with NAMD+VMD and GAUSSIAN/ORCA

Instructor:

Pedro Ojeda

Helper:

Birgitte Brydsö

Initial instructions:

cd /proj/nobackup/qmmm2021
mkdir username   #or any name you like
git clone https://github.com/hpc2n/course-qmmm.git 
cd course-qmmm/