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QM/MM - best practices

QM/MM - best practices

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!


PRELIMINARY AGENDA

09:00 - 10:00 Lecture on classical MD simulations
10:00 - 10:05 Break
10:05 - 11:00 Setting up a MD simulation with QwikMD (VMD plugin)
11:00 - 11:05 Break
11:05 - 12:00 Setting up a MD simulation on the VMD TK terminal
 
12:00 - 13:00 Lunch
 
13:00 - 14:00 Lecture on QM/MM simulations
14:00 - 14:05 Break
14:05 - 15:00 Setting up a QM/MM simulation with QwikMD (VMD plugin)/ORCA
15:00 - 15:05 Break
15:05 - 16:00 Setting up a QM/MM simulation on the VMD TK terminal/GAUSSIAN
 

Materials and recording

The presentations and materials can be downloaded here: https://github.com/hpc2n/course-qmmm

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.

Course project

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:

  • You may be given access to the project before the course; please do not use the allocation for running your own codes in. Usage of the project before the course means the priority of jobs submitted to it goes down, diminishing the opportunity for you and your fellow participants to run the examples during the course. You can read more detailed information about the job policies at HPC2N here.
  • The course project will be open 1-2 weeks after the course, giving the participants the opportunity to test run examples and shorter codes related to the course. During this time, we ask that you only use it for running course related jobs. Use your own discretion, but it could be: (modified) examples from the hands-on, short personal codes that have been modified to test things learned at the course, etc.
  • Anyone found to be misusing the course project, using up large amounts of the allocation for their own production runs, will be removed from the course project.

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!

 

Updated: 2022-11-01, 14:32