Tehdyt toimenpiteet
Running Gromacs jobs in Grid Environment
The purpose of the workshop is to present the Grid resources available in the Nordic countries and give the participants the basic knowledge to access these resources. See also http://www.nordugrid.org/
The workshop will also present in detail several examples on how to perform molecular dynamics simulations using the Gromacs software (http://www.gromacs.org) in the Grid. This aims at providing more computational resources and alternative approaches to the scientists. During the workshop Gromacs developers are available to answer other Gromacs specific questions.
The workshop in intended for people with little or no previous Grid-experience, at least some experience on Gromacs, and basic linux/unix command line knowledge.
The event is sponsored by the Nordic Grid Data Facility (NDGF).
Program
Wednesday 14.11.
14:00 - 18:00 Registration, Gromacs and Grid introduction, theory
Berk: How to run Free energy simulation with Gromacs (pdf)
Erik: Introduction to Molecular simulations and parallelization (pdf, 17MB)
Erik: Case studies on potential of mean force simulations (pdf, 10MB)
ARC-grid introduction slides (pdf)
ARC-grid tutorial exercises (pdf)
18:00 - Dinner, Sauna
Thursday 15.11.
09:00 - 12:00 Grid exercises, Gromacs hands-on
Free energy of solvation for ethanol (tar.gz)
12:00 - 13:00 Lunch
13:00 - 16:00 Hands-on continued and wrap up
Exercise topics: Free Energy simulations (Potential of mean force) using constraints, pulling, and topology mutation , Principal component analysis, folding, ...
- 35 euros + VAT (22%) for Finnish academics
- 70 euros + VAT (22%) for governmental research institute staff
- 105 euros + VAT (22%) for others
Registration
Additional information
Some links for accommodation in Espoo (walking distance):
Radisson SAS Otaranta
In Helsinki centre (~15 minutes by bus):
Suggested by the Tourist office
Ten rooms have been pre-reserved in Hotel Hanasaari (100 EUR/single, 142 EUR/double) where also the Wednesday's dinner and sauna take place. Please book your room by email (myyntipalvelu at hanaholmen.fi) or phone (+358 9 43502411)
and mention that you're participating in CSC:s Grid-Gromacs event.
What to do in Helsinki? -> Helsinki This Week
Financial support
Participants coming outside Finland may apply for partial reimbursement for travel expenses. If you plan to apply for support, please estimate the costs (flights, trains, accommodation) and send them to atte.sillanpaa at csc.fi. The reimbursements are paid to your bank account based on receipts of the travel expenses after the workshop.
