Tehdyt toimenpiteet
Gromacs Workshop at CSC 2007
This is the homepage of the three day Gromacs Workshop starting on 27th February 2007, in Espoo, Finland. (60°10'42.09"N, 24°49'58.94"E)
Lecturers
The talks and the hands-on sessions were be given by Erik Lindahl, David van der Spoel, and Berk Hess. On Tuesday and Wednesday these will be supplemented by contributed talks from the participants.
Program
The program outline is presented below. On Monday before the actual Workshop, which starts on Tuesday, there will be a basic tutorial for using Gromacs. The talk videos will be added on the site shortly.
The talks and tutorial files can be accessed also here.
| time | Monday 26.2. Pre workshop tutorial |
|---|---|
| 13:15-13:30 |
Registration |
| 13:30-14:15 | Introduction to molecular modeling: Theoretical framework, modeling levels, limitations and possibilities, systems and methods (Erik) (Slides, pdf) (Video, rm) |
| 14:15-14:30 | Coffee |
| 14:30-15:15 | Molecular dynamics simulations & Gromacs introduction: Force fields, integrators, control of temperature and pressure (Berk) (Slides, pdf) (Video, rm) |
| 15:30-16:30 | Hands-on simulation & analysis: First a simple liquid (water), and then a protein solvated in water (Hands-on files, html/tar) |
| 17:00- | Mixer |
| time | Tuesday 27.2. Workshop day 1 |
|---|---|
| 09:00-09:15 |
Registration |
| 09:15-10:10 | Analysis of MD trajectories in GROMACS (David) (Slides, pdf) (Video, rm) |
| 10:10-10:40 | Coffee |
| 10:40-11:35 | Free energy calculations (Berk) (Slides, pdf) (Video, rm) |
| 11:35-12:30 | Contributed talks Tomas Kubar: "Free-energy calculations and the study of DNA..ligand interactions" (Slides, ppt) (Video, rm) Maxim Fedorov: "What effects do salts have on biopolymers?" (Slides, ppt) (Video, rm) |
| 12:30-13:30 | Lunch |
| 13:30-16:30 | hands-on: Analysis tools (Hands-on files, html) hands-on: Potential of mean force calculations (hands-on files, tar) hands-on: Free energy of solvation (Hands-on files, tar) |
| 16:30-17:30 | Poster Session |
| time | Wednesday 28.2. Workshop day 2 |
|---|---|
| 09:15-10:10 | Speeding up Simulations: Algorithms & Applications (David) (Slides, pdf) |
| 10:10-10:40 | Coffee |
| 10:40-11:35 | Membrane simulations (Erik) (Slides, pdf) (Video, rm) |
| 11:35-12:30 | Contributed talks Søren Enemark "Tubulin Monomer Mechanical Properties obtained by simulating Atomic Force Microscopy experiments using Molecular Dynamics" (Slides, ppt) (Video, rm) Perttu Niemela: "Assessing the Nature of Lipid Raft Membranes" (Slides, ppt) (Video, rm) |
| 12:30-13:30 |
Lunch |
| 13:30-16:30 | hands-on: Analysis tools (Hands-on files, html) hands-on: Potential of mean force calculations (hands-on files, tar) hands-on: The pull package (Hands-on files, tar) |
| ~20:00- | Dinner in Östrabotnia |
| time | Thursday 1.3. Workshop day 3 |
|---|---|
| 09:15-10:10 | Gromacs development. Installing the CVS version and using advanced features (Erik) (Slides, pdf) (Video, rm) |
| 10:10-10:40 | Coffee |
| 10:40-11:35 | Building your own Linux cluster for Gromacs (and other programs) (Erik) (Slides, pdf) (Video, rm) |
| 11:35-12:30 | Birds-of-a-Feather: ask about the Gromacs, the Universe, and Everything. |
| 12:30-13:30 |
Lunch |
| 13:30-16:30 | hands-on: Parallel simulations in practice (Hands-on files, html) hands-on: The gory details: Understanding and hacking the Gromacs source (Hands-on files, html) hands-on: Help with your own code or simulations |
| 16:30 | Workshop over |
The book of abstracts
The Workshop participants, the program and abstracts for the contributed talks and posters are collected in this Book of Abstracts (pdf).
If you're interested, have a look at the previous course on 2004 here: Gromacs Workshop 2004
The course is arranged in collaboration with the ISB - National Graduate School in Informational and Structural Biology.
A few pictures from the hands-on sessions: pic1, pic2, pic3 (pictures taken by Jyrki Hokkanen, CSC)
See also
Gromacs homepage: www.gromacs.org
