Gromacs 5 - Training
CSC Koulutukset ja tapahtumat ovat muuttaneet
Löydät tulevat koulutukset ja tapahtumat osoitteesta www.csc.fi/asiakaskoulutus.
Tämä sivusto on arkistoversio eikä sitä enää päivitetä
Päiväys: | 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. |
Kieli: | english-language |
lecturers: |
Dr. Hector Martinez-Seara Tampere University of Technology Dr. Atte Sillanpää CSC Dr. Martti Louhivuori CSC |
Hinta: |
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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. |
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.
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