High Performance Computing Center North
The aim of the 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 Biomolecular (protein+water) 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 software already installed at HPC2N, i.e. 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.
This course will be one-day. 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!
The course was recorded (lectures) and can be seen on HPC2N's YouTube channel: https://youtube.com/playlist?list=PL6jMHLEmPVLzrmSfqoCQsIf-8nRKh3dLB
Participation is free and open to all users from the SNIC HPC centres and academics throughout the Nordic region.
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.
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:
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.
Requirements: A previous knowledge of HPC2N cluster, LINUX. NOTE: if you want to follow the exercise with ORCA software, please follow the requirements on our website (https://www.hpc2n.umu.se/resources/software/orca) for being added to the ORCA group.
Instructor: Pedro Ojeda May
Time and date: 9 December 2021, 09:00-16:00.
Location: ONLINE (Zoom).
Deadline for registration: 1 December 2021
Please register using this form. All fields marked with * are mandatory. REGISTRATION CLOSED!