[ONLINE] Introduction to GROMACS - A SNIC/PRACE workshop in collaboration with BioExcel

Europe/Stockholm
On line

On line

Description

GROMACS (www.gromacs.org) is a free, open-source and high-performance software suite for molecular dynamics simulation and analysis.The workshop will provide an introduction to use of  GROMACS. The course will be delivered by KTH staff.

The workshop aims to provide the basis to perform molecular dynamics simulations and simple free energy calculations using GROMACS.

The workshop will include online lectures and hands-on sessions on the following topics:

  • The basics of molecular dynamics simulations
  • Introduction to free energy calculations
  • The capabilities of GROMACS 

During the hands-on computer practicals you will work on protein simulation and solvation free energy using GROMACS.

The workshop is organized jointly by PRACE, the main HPC resource provider in Europe, BioExcel, the leading European Center of Excellence for Computational Biomolecular Research and SNIC, Swedish National Infrastructure for Computing.

Prerequisites

The workshop is at beginners level and assumes no prior experience in GROMACS.

The participants are excepted to remotely attend the whole workshop. Zoom will be used to run the workshop remotely.

The participants need to have access to a computer where the following software were already installed: Jupiter notebook,  GROMACS, VMD (visualisation), Xmgrace (plotting tool) to actively follow the tutorial. More information after registration.

Registration will open 22nd June 2020.  Note the workshop is full, but you are welcome to register to the waiting list, using the link below.   Last registration day: 31 July 2020. 

number of participants: 30 max 

Preliminary Schedule

Thursday 3 September 2020 (Day I)

  • 09:00    Welcome 
  • 09:10-10:10 lecture I + Q&A session
  • 10:10-10:40 break 
  • 10:40-11:40 lecture II + Q&A session
  • 11:40-13:00 lunch
  • 13:00-14:30 tutorial
  • 14:30-15:00 break 
  • 15:00-16:00 lecture III  + Q&A session

Friday 4 September 2020 (Day II)

  • 09:00-10:00 lecture IV + Q&A session
  • 10:00-10:30 break 
  • 10:30-11:30 lecture V + Q&A session
  • 11:30-13:00 lunch
  • 13:00-15:00 tutorial
  • 15:00-15:30 final remarks  

Course material

All the course material will be available online. 

Contact

For more information, contact Alessandra Villa 

 

Alessandra Villa
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