Tehdyt toimenpiteet
Coarse Graining Workshop 2009
In this workshop, some of the leading developers of coarse-grained models present the fundamentals of coarse graining as well as examples of applications where coarse-grained models have been applied to elucidate complex processes in biosystems. Additionally, after the morning lectures, the afternoons are spent with hands-on exercise sessions based on the lectures given earlier.
For practical reasons, the workshop, and especially the exercises will be based on using Gromacs together with the MARTINI model [1-4] that allows large-scale simulations of systems comprised of e.g. lipids and proteins. Consequently, the participants are expected to know the basics of molecular dynamics and the Gromacs molecular dynamics software. Those eager to participate in this meeting without previous experience of using Gromacs can familiarise themselves with this program by doing some simple exercises, such as those available in the tutorial section at the Gromacs homepage (www.gromacs.org).
In addition to the invited lectures, there are contributed talks by the participants. Poster sessions will not be organized.
Downloadable stuff
The lecture slides have been added to the program below. The material is linked also on the folllowing pages: The instructions and input files needed in the exercises are available here. Example output for different tutorials are available here.
A few Photos
from the refreshments, hands-on exercises, machine room and Siewert-Jan announcing the Multi Scale Modeling of Soft Matter Symposium in the summer (see web site).
[1] SJ Marrink et al. J Phys Chem B 108 (2004) 750; cited 190 times.
[2] SJ Marrink et al. J Phys Chem B 111 (2007) 7812.
[3] L Monticelli et al. J Chem Theory Comput 4 (2008) 819.
[4] http://md.chem.rug.nl/~marrink/coarsegrain.html
Program
| time | Wednesday, January 28, 2009 Basics and Lipids |
|---|---|
| 09:00-09:10 | Atte Sillanpää and Ilpo Vattulainen: Welcome and Practical Matters |
| 09:10-09:50 | Alex de Vries: Introduction to MD and Multi-scale Modeling (Slides, pdf) |
| 09:50-10:30 | Berk Hess: Introduction to GROMACS and its Recent Development |
| 10:30-11:00 |
Coffee |
| 11:00-11:45 | Alex de Vries: Theoretical Background of Coarse Graining, Hierarchical Modeling, and the Related Caveats (Slides, pdf, same as above) |
| 11:45-12:30 | SJ Marrink: Philosophy of the MARTINI Model - with Lipids & Applications (slides, pdf) |
| 12:30-12:45 | Alex de
Vries: Overview of the hands-on exercises |
| 12:45-14:00 | Lunch & Free Discussion |
| 14:00-16:00 | Tutorials: Lipids (Tutorial files) |
| 16:00-16:15 | Coffee |
| 16:15-18:00 | Tutorials: Lipids continues |
| time | Thursday, January 29, 2009, Proteins |
|---|---|
| 09:00-09:45 | Alex de Vries: Validation of Coarse Grained
Models Against Atomistic Ones, incl. Mapping and Reverse Mapping (Slides, pdf) |
| 09:45-10:30 | Luca Monticelli: MARTINI Model for Proteins (slides, pdf) |
| 10:30-11:00 | Coffee |
| 11:00-11:45 | Luca Monticelli: MARTINI Applications for
Peptides & Nanomaterials (slides, pdf) |
| 11:45-12:30 | SJ Marrink: MARTINI Applications for Proteins
and Peptides (slides, pdf) |
| 12:30-14:00 | Lunch & Free Discussion |
| 14:00-16:00 | Tutorials: Proteins (Tutorial files) |
| 16:00-16:15 | Coffee |
| 16:15-17:45 | Tutorials: Proteins continues |
| 18:00 | Bus departs to Sauna + Dinner |
| 18:30-23:00 | Get-together at the Sauna Premises of the Helsinki Police Society |
| time | Friday January 30, 2009, PMF and MARTINI extensions |
|---|---|
| 09:00-09:45 | Berk Hess: Coarse Graining Through PMF's with
Theory and Applications (slides, pdf) |
| 09:45-10:30 | SJ Marrink: MARTINI Model for Carbohydrates
& New Ideas. View for How to Develop MARTINI Force Fields for Your Own
Molecule (slides, pdf) |
| 10:30-10:45 | Teemu Murtola: Improved Analysis of Gromacs trajectories
- Dynamic Selections and Library Functions (slides, pdf) |
| 10:45-11:00 | Samuli Ollila: 3D Pressure Field in Lipid Membranes
and Membrane-Protein Complexes (slides, pdf) |
| 11:00-11:30 | Coffee |
| 11:30-11:45 | Alexander Lyubartsev: Systematic Coarse-Graining of
Molecular Models by Inverse Monte Carlo (slides, pdf) |
| 11:45-12:00 | Sergio Pantano: A Transferable, Accurate and Unbiased
CG Model for Simulating RNA (slides, pdf) |
| 12:00-12:15 | Outi Lampela: Coarse-grained Calculation of the
Molecular Polarizability of Proteins (slides, pdf) |
| 12:15-12:30 | Dominik Fritz: From Atomistic to Mesoscale Systems Without Fitting: A Coarse Grained Model for Polystyrene |
| 12:30-12:45 |
Andrea Danani: Multiscale Modeling Applied to Polymer-Clay
Nanocomposites (slides, pdf) |
| 12:45-13:00 |
Godehard Sutmann: Multi-Particle Collision Dynamics on Massively Parallel Computers (slides, pdf) |
| 13:00-14:00 | Lunch & Free Discussion |
| 14:00-16:00 | Tutorials: PMF Tutorials, Participants' own MARTINI models, and Lipids & Proteins (Tutorial files) |
| 16:00-16:15 | Coffee |
| 16:15-18:00 | Tutorials: Lipids & Proteins with Participants' Own Models |
Registration
Additional information
Preparing your laptop for the hands-on exercises
We can offer a workstation for 12 pairs of participants (i.e. two sharing a workstation) but the rest must use their own laptops to perform the hands-on exercises. The best setup is to have the following programs installed on your laptop:
- Gromacs (version 3 and/or 4) (download link)
- Fortran compiler
- python
- Xmgrace (download link)
- VMD (download link)
- DSSP (download link)
If you can't or don't want to install these on your laptop, you can use them remotely from our computing server. There may be some delay in the graphical x-connection, but the ascii-terminal will work smoothly. Note, that you'll need an x-terminal/emulator in your laptop. We recommend X-ming, if you don't have one yet.
If you don't want to install everything, please consider installing at least VMD, as it suffers most from running it remotely.
How to get to CSC?
From Airport take a bus (615) to the city center and then follow these instructions. In a hurry take a taxi from the airport directly to CSC (up to 40 minutes).
Accommodation
Finding last minute accommodation at reasonable price may be difficult in Helsinki. Consider booking early. Some links for accommodation in Espoo (walking distance):
Radisson SAS Otaranta
In Helsinki centre (~15 minutes by bus):
Suggested by the Tourist office
What to do in Helsinki?
Climate
Bring warm clothes. In January there should be some snow on the ground and temperatures typically below zero. You can check the Finnish Meteorological Institute pages for current weather in Helsinki and average January weather in Finland (tammikuu=January... ).
Hands-on practicals
The maximum number of participants for hands-on exercises is 60. The lectures can be attended by 130 people. The hands-on exercises will be divided into two rooms. The computer room has 12 workstations, 2 seats for each, so that two people share one workstation. The other room only provides an internet connection (to the computing servers) and therefore the participants are required to bring their own laptops. The other room can accommodate 34 people with their own laptops. The exercises can be done on your own laptop/workstation, but if you want, there are also some resources on our supercomputers Louhi and Murska and you only need ssh and an x-terminal on your laptop to log on those. Therefore, it will be very useful to have gromacs and the analysis software installed on your laptop (see above).
In addition to the lecturers you'll get help from Martti Louhivuori, Samuli Ollila, Andrzej Rzepiela and Lars Schaefer during the hands-on exercises.
Contributed talks
If you want to give a short talk (15 min) concerning some aspects of coarse graining, like a case study, please tick the corresponding checkbox in the registration form and send the title and abstract to atte.sillanpaa at csc.fi preferably by the end of November. We may consider talks also after this.
Organisers
The workshop is organised by Dr. Atte Sillanpää (CSC - The IT Center for Science Ltd.; atte.sillanpaa at csc.fi) and Prof. Ilpo Vattulainen (Tampere University of Technology; ilpo.vattulainen at tut.fi).
Flyer
Print this flyer (pdf) and put in on your notice board!
Sponsors
The workshop is supported by the National Graduate School in Materials Physics in Finland (http://www.fyslab.hut.fi/gradschool/) and the National Graduate School in Informational and Structural Biology (http://www.abo.fi/isb).
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