Training and Eventsadvanced-gromacs-workshop - Training
| Date: | 09.10.2019 12:00 - 11.10.2019 13:00 |
| 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. Christian Blau Theoretical and Computational Biophysic KTH Royal Institute of Technology Dr. Rodrigo Vargas Honorato computational structural biology group Utrecht University |
| Price: |
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| The fee covers lunches as well as morning and afternoon coffees and social program. |
Practicalities: event-support@csc.fi
The worshop will introduce HADDOCK, (High Ambiguity Driven protein-protein DOCKing) which is an information-driven flexible docking approach for the modeling of biomolecular complexes, and PMX which is a service for users who need to do free energy calculations. PMX utilizes the Gromacs classical molecular dynamics simulation engine to perform calculations at the background. The workshop also covers advanced usage of Gromacs itself in particular on HPC environment.
Upon registration the participants are asked for special topics they are interested in which potentially could be covered at the workshop. It will be possible to follow a video stream of the lectures also remotely, but unfortunately we will not be able to support doing the hands-on remotely. You can install and test your setup in here: http://zoom.us/test and join the Stream in here: https://cscfi.zoom.us/j/793265414
BioExcel can provide a limited number of travel bursaries for participants. Instructions to apply can be found in the registration form.
The event is organized in collaboration with BioExcel and CSC and supported by PRACE.
Remote participation
We will stream the lectures via Zoom, https://cscfi.zoom.us/j/793265414 Questions via chat. Starting at around 13 EEST.
Wednesday 9th October
11:30-12:00 Registration - training room lounge
12:00 Lunch
13:00 Gromacs - where are we now, what's new, what's coming in the future
14:00 Maximizing Gromacs performance for HTC and HPC
14:30 Hands on - Performance
15:00 Advanced simulation protocols in GROMACS
15:30 Hands on - Advanced simulation protocols
18:00 Light dinner and Flash talks
21:00 End of Day 1
Thursday 10th October
9:00 PMX - alchemical free energy calculation setup tools introduction
10:00 Hands on - PMX github.com/deGrootLab/pmx
12.00 Lunch
13:00 HADDOCK – Modelling intermolecular interactions
14:00 Hands on - HADDOCK www.bonvinlab.org/education/HADDOCK24/
15:00 HADDOCK – advanced topics
17:00 End of day 2
Friday 11th October
9:00 Getting deeper into issues and questions that emerged during the workshop, performance
10:00 Participant contributions, Q&A, Discuss your own model systems
12:00 Lunch
13:00 Closing
