Gromacs

Goettingen 2008 Workshop

    Workshop on Gromacs and Advanced Simulation Methods

    Max Planck Institute for Biophysical Chemistry

    September 24th-26th, 2008

    Background

    We are happy to announce the second special GROMACS workshop together with Helmut Grubmueller & Bert de Groot at the Max Planck Institute for Biophysical Chemistry in Goettingen, Germany. As in the previous workshop at Stanford Universiy, the scope of this workshop is to gather people working on new or otherwise advanced simulations algorithms, either in- or outside GROMACS, but

    that we believe could be interesting to support in the future. In contrast to the previous tutorials given e.g. in Helsinki, we will assume that the participants here are fairly comfortable with Gromacs, or at least MD simulations in general. We are planning three full days with a mix of formal talks, birds-of-a-feather sessions, hands-on tutorials and question-and-answer sessions in smaller groups. The main GROMACS developers plan to be present.

    Topics Covered

    There are a couple of interesting topics that we have already selected:

    • The new domain decomposition parallelization in Gromacs 4.0, with some tips & tricks to get the most out of your hardware.
    • MD of very large systems
    • Non-Equilibrium MD/Force probe simulations
    • Validation of simulation by experiment and vice versa
    • QM/MM. How do you mix Quantum Mechanics with Gromacs?
    • Virtual sites for hydrogen motion removal and long time-steps
    • Membrane protein simulations
    • Replica exchange
    • Gromacs source code walk-through

    However, these are just examples. We would be particularly interested in participants who would like to contribute a small talk (anywhere from 15 to 30 mins) on their favorite subject, or if you have special requests about topics you'd like to learn more about.

    Location

    The workshop will be given in Max Planck Institute

    for Biophysical Chemistry, Am Fassberg 11, D-37077 Goettingen, Germany. For more information and directions, have a look at http://www.mpibpc.mpg.de/english/institut/anfahrt/index.html .
    We start in the large seminar room in the administration building on Wednesday September 24 at 9:00 am, and finish on Friday Septeber 26 at 5:00pm.

    Program

    Wednesday 24 September

    09:00 Welcome Gerrit Groenhof

    09:15 Helmut Grubmueller TBA

    10:05 Mareike Zink Simulation of a complete viral shell: The mechanical properties of icosahedral viruses

    10:30 Coffee/tea

    10:50 Berk Hess Domain decomposition in gromacs 4.0

    11:35 Carsten Kutzner Improving PME on distributed computers systems

    12:00 Carlo Camilloni GroMeta: metadynamics in gromacs

    12:25 Gerrit Groenhof QM/MM capabilities of Gromacs

    13:00 Lunch

    14:00 Ran Friedman A phenomenological coarse-grained model for membrane simulations

    14:25 Nicolae Goga Developments in multiscale modelling

    14:50 Florian Dommert Multiscale approach for force field parametrization for ionic liquids

    15:15 Andzej Rzepiela Reconstruction of atomistic details from coarse grained simulations

    15:40 Coffee/tea

    16:00 Erik Lindahl Pushing your simulation performance with gromacs

    16:40 Jocelyne Vreede Conformational transitions of the Photoactive Yellow Protein

    17:05 Erik Brandt Dynamic structure factors from lipid membrane molecular dynamics simulations

    17:30 Discussion and concluding remarks

    Thursday 25 September


    09:00 Bert de Groot TBA

    09:40 Luca Monticelli Calgary Lipids: a lipid forcefield for biomolecular simulations

    10:05 Martti Louhivuori Osmotic shock induced gating of a mechanosensitive channel in a vesicle

    10:30 Coffee

    10:55 Durba Gupta Association of membrane proteins: simulations and free energy calculations

    11:20 Peter Kasson Large-scale simulation of membrane fusion and influenza host-ligand recognition

    11:45 Lieven Butts Allosteric unlocking of a prokaryotic toxin by an intrinsically disordered antidote

    12:10 Maximilian Andrews Effect of temperature on the structural and hydrational properties of human islet amyloid polypeptide in water

    12:35 Michel Cuendet Protein-protein interactions investigated by steered molecular dynamics

    13:00 Lunch

    14:00 David van der Spoel Force Fields Forever

    14:50 Erik Lindahl Gromacs source code build system walk-through

    15:40 Tea/Coffee

    16:00 Code kitchen – discuss your code with the experts

    17:00 Discussion/Concluding remarks

    Friday 26 September

    09:00 Michael Shirts Free energy calculations using Gromacs: examples and future possibilities in gromacs

    09:40 Serena Donnini Constant pH simulations with gromacs

    10:05 Ollila Samuli 3D pressure profiles

    10:30 Coffee/tea

    10:55 Esteban Voehringer-Martinez TBA

    11:20 Daniel Larsson The big picture: Simulation of a virus particle

    11:45 Jochen Hub TBA

    12:10 Tsjerk Wassenaar Better use (of) periodic boundary conditions

    12:35 Michele Seeber TBA

    13:00 Lunch

    14:00 Tutorials (maybe), Discussion, Code kitchen, … Details will follow.

    17:00 Closing

    Travel and Accommodation

    The easiest way to reach Goettinen

    is to fly to Hannover (HAJ) or Frankfurt (FRA). From both airports there is a good railway connection with the Deutsche Bahn (DB) to Goettingen. From the main station, you can either take the bus (line 5) or taxi (10 euro's) to reach the institute or the hotel.

    We have reserved a number of rooms in hotel Beckmann for the duration of the workshop. The hotel is a 15 minutes walk from the institute. There is a bus connection to downtown Goettingen every 30 minutes. You will have to make a reservation yourself, but use the group code "GROMACS Workshop" to get a lower rate.

    The hotel rooms are EUR 44.00 per night for singles, and EUR 74.00 per night for doubles. Please share rooms if you can/want, since we could only reserve a limited number of rooms.

    In case Beckmann is booked full, your other options are:

    Clarion Parkhotel Goettingen
    Kasseler LandStrasse 45
    D-37081 Goettingen
    tel: +49(0)551 902402
    fax: +49(0)551 902166
    info@clarion-hotel.de

    Or

    Best Western Hotel Am Papenberg
    Hermann-Rein-Straße 2
    37075 Göttingen
    tel: +49(0)551-30550
    fax: +49(0)551-3055400

    Cost?

    It's free! However, you will have to take care of

    your own travel, accommodation and food.

    Other questions

    Please contact Gerrit Groenhof

    on ggroenh@gwdg.de, or ask on the gmx-users mailing list.

    Registration Info

    Typically we would simply say "first come,

    first served", but we will give priority to participants who are willing to give brief presentations (remember, we want this to be two-way communication!) as long as they register the first two days.
    Thus, start by filling in the form below, and wait for a confirmation email. Note that we the first round of confirmations won't be sent until 1st of June, so we can do random selection based on the priorities above, just in case there is a gold-rush of early birds.
    After that it will be first-come, first-served.
     

    While registration isn't binding, we ask you to only register if you will take part in the entire workshop (you are welcome to drop by anyway :-), and please let us know as soon as possible if you change your mind and decide not to come, so somebody else can use your slot!

    Registration Form

    Registration is closed (Friday 6th June).


    Once again, very welcome to the workshop, and hope to see you in Goettingen in September!



    --



    Berk Hess


    Erik Lindahl


    David van der Spoel


    Carsten Kutzner


    Gerrit Groenhof


    Bert de Groot


    Helmut Grubmueller

    Page last modified 08:38, 15 Mar 2009 by rossen