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Gromacs 5

Gromacs 5
Date: 24.11.2015 9:00 - 24.11.2015 17:00
Location details: The event is organised at the CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. The best way to reach us is by public transportation; more detailed travel tips) are available.
Language: english-language
lecturers: Dr. Hector Martinez-Seara
Tampere University of Technology
Dr. Atte Sillanpää
CSC
Dr. Martti Louhivuori
CSC
Price:
  • 60 for-finnish-academics
  • 280 for-others
The fee is 60 EUR/day and covers all materials, lunches as well as morning and afternoon coffees. Contact event-support (ät) csc.fi for further information.
registration-closed
The seats are filled in the registration order. You may cancel your attendance without a charge 5 business days prior the course. For cancellations after that and no-shows without a cancellation the full fee will be invoiced.

Monday, November 23rd – INTRODUCTION TO GROMACS

1. What files do I need to run a simulation in Gromacs and how I generate them
2. Running Gromacs jobs at CSC's servers
3. Analysing results with Gromacs tools

Learning outcome: the participants know how to efficiently run standard Gromacs jobs on CSC's servers.

Prerequisites: basic understanding of molecular dynamics, basic Linux skills. If unsure, you can prepare e.g. by scanning these materials in advance. MD intro in Spring School in Computational Chemistry 2015, Introduction to Linux.

Program

The workshop starts on Monday at 9 and ends at 17.

Monday, November 23rd – INTRODUCTION TO GROMACS

1. What files do I need to run a simulation in Gromacs and how I generate them

  • What is the gmx tool and how it is used
  • Using charmm GUI to create a membare topology
  • Prepare a protein for simulation starting from downloading it from the pdb data bank

2. Running Gromacs jobs at CSC's servers

  • Explanation of different types of Gromacs files
  • Useful web resources in preparing Gromacs simulations
  • Notes of force fields
  • Run Gromacs simulations
  • Optimize simulation setup for performance

3. Analysing results with Gromacs tools

  • How to check for correctness, observing trends and drifts, compare with experiments

If you want some special topic to be included in the program, please contact atte.sillanpaa [ät] csc.fi

CSC Gromacs page: research.csc.fi/-/gromacs

Gromacs home page: gromacs.org

Course materials
Hands on exercises » Lecture slides (Hector) » Lecture slides - Using Gromacs at CSC »
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