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ESPResSo Summer School 2013

Simulating Soft Matter with ESPResSo, ESPResSo++ and VOTCA

October 7,  2013 to October 11, 2013

Institute for Computational PhysicsStuttgart University, Germany

 


Participants and Speakers of the ESPResSo Summer School 2013.

Participants and Speakers of the ESPResSo Summer School 2013.

ESPResSo ESPResSo++ and VOTCA are open-source program packages that have been designed specifically to study coarse-grained soft matter systems, and they are used by more than 100 institutions worldwide. The packages are developed at the ICP at Stuttgart University, Germany and the Max-Planck-Institute for Polymer Research in Mainz, Germany. All three applications are tools that make it significantly easier for PhD students and researchers in general toget started with their projects.

Between October 7-11, ICP, the SimTech Cluster of Excellence at Stuttgart  University and CECAM (Centre Européen de Calcul Atomique et Moléculaire) organize the SimTech-CECAM-ESPResSo Summer School 2013. The school provides a detailed and hands-on introduction to the software packages and their uses.

The school consists of Lectures and Hands-on Sessions, both for beginners as well as for experienced users and developers of ESPResSo, ESPResSo++ and VOTCA. The introductory sessions aim to introduce the general ideas and usage of ESPResSo and its most common features for the simulation of a broad variety of soft matter systems. The advanced sessions are offering a more in-depth look into the code of the software and additional algorithms and possibilities of ESPResSo++, VOTCA and ADResS. It is aimed to attract researchers who are already familiar with the basic ESPResSo features and want to build on that or want to extend and optimize the code to better match their simulation setups.

Furthermore, there will be a Poster Session and Lightning Talks where participants have the opportunity to present their projects and ideas with the other participants and the speakers, and a number of Scientific Talks where scientists will present recent research projects that were done with any of the software packages. Another aim of this school is to give the developers of the software packages feedback on ongoing research on soft matter, so that design decisions better match the needs of the community.

Poster of the ESPResSo Summer School 2013

Poster of the ESPResSo Summer School 2013

To apply and register for the summer school, please send an informal email to ess@icp.uni-stuttgart.de. In the mailing, please include the following information:

  • full name and affiliation (for the name tag)
  • work address (for us to report to CECAM)
  • level of experience with ESPResSo or ESPResSo++:
    • “I am a beginner.”
    • “I have written a Tcl/Python script for ESPResSo or ESPResSo++.”
    • “I have had a look at the C-code of ESPResSo or ESPResSo++.”
    • “I have done modifications or extensions to the code of ESPResSo or ESPResSo++.”

(Non-)Support and (Non-)Fees

  • Unfortunately, we are not able to provide financial support for travel or accommodation. You will have to access your own funding sources to cover these costs.
  • There are no fees for the school itself.
  • The following things are included for participants of the school
    • Lunches (Monday to Friday)
    • Coffee breaks and snacks (Monday to Friday noon)
    • BBQ on Tuesday evening

Travel and Accommodation

  • You will have to book your accommodation in Stuttgart yourselves. However, we have reserved a number of rooms (singles and doubles) in the International Student Hostel (from 25.50€ for students). Use the keyword “Espresso” to get one of the rooms from our contingency.[important]Please book your rooms as soon as possible, as the reservation are only valid for a limited time![/important]
  • If the rooms in the International Student Hostel are all occupied, consider the ETAP hotel in Stuttgart.
  • Stuttgart can be reached by plane (airport code STR) or by train (“Stuttgart Hauptbahnhof”). Both from the train station and the airport the ICP as well as the ETAP hotel can be reached easily by public transport. Details will follow on this page.

Poster Session and Lightning Talks

We want to give the participants ample opportunity to present their own work and ideas.

  • On Monday evening (17:00-18:00), we will have Lightning Talk Session of one hour, where people can present a very short talk. Lightning talks are intended to present finished and unfinished ideas of projects to be discussed with interested people afterwards, or to tease people to your poster. Depending on how many people want to give a lightning talk, the time per talk will be adapted (probably something between 5 and 20 minutes). If you want to give a lightning talk, please send an email with the title to ess@icp.uni-stuttgart.de.
  • We will hold a Poster Session (and a BBQ) on Tuesday evening where most people from our institute will put up their posters. If you have a poster that you would like to present, just bring it along! Note that the posters can most probably stay mounted on the poster walls during the whole school.

Further Details

  • If you have a Laptop, please bring it along! We will have some desktop computers where you can do the hands-on sessions, but we recommend to bring your own machine. It should provide some kind of POSIX OS (i.e. basically anything but Windows).
  • On Wednesday evening, we will have a Conference Dinner. Unfortunately, we cannot fund the dinner for the participants, but only for the speakers. Participants are invited to join the dinner, anyway.
  • The school will end on Friday by 13:00, so that most people can still travel home on Friday. From ICP to Stuttgart airport you will need about 30 minutes.

Monday, October 7th

8:30 – 9:00 Registration
9:00 – 9:30 Welcome
Olaf Lenz (ICP Stuttgart, Germany)
[talk.pdf]
9:30 – 10:30 Lecture
Introduction to Soft Matter Simulations
Christian Holm (ICP Stuttgart, Germany)
[talk.pdf]
10:30 – 11:00 Coffee Break
11:00 – 11:30 Lecture
Speeding up and Parallelizing Molecular Dynamics Simulations
Olaf Lenz (ICP Stuttgart, Germany)
[talk.pdf]
11:30 – 12:30
Track 1: Lecture
Introduction to ESPResSo and Tcl
Olaf Lenz (ICP Stuttgart, Germany)
[talk.pdf]
Track 2: Lecture
Introduction to ESPResSo++ and Python
Torsten Stühn (MPIP Mainz, Germany)
[talk.pdf]
12:30 – 14:00 Lunch break
14:00 – 17:00
Track 1: Lecture and Hands-On
Introduction to ESPResSo and Tcl (Part 2)
Olaf Lenz (ICP Stuttgart, Germany)
[talk.pdf] [worksheet.pdf]
Sample scripts: [lj.tcl] [stretched_polymer.tcl]]
Track 2: Lecture and Hands-On
Introduction to ESPResSo++ and Python (Part 2)
Torsten Stühn, Vitalii Starchenko (MPIP Mainz, Germany)
[talk.pdf] [Tutorial]
Track 3: Hands-On
ESPResSo : Under the Hood
Stefan Kesselheim, Rudolf Weeber (ICP Stuttgart, Germany)
17:00 – 18:00 Lightning Talks

Tuesday, October 8th

9:00 – 11:15
Lecture
Top-Down Modelling

  • Modelling coarse-grained membranes
    Patrick Diggins (Carnegie-Mellon University, USA)
    [talk.pdf]
  • Modelling two-phase flow
    Marcello Sega (University of Vienna, Austria)
    [talk.pdf]
  • Modelling soft bodies with immersed boundaries
    Markus Gusenbauer (University of Applied Sciences, St. Pölten, Austria)
    [talk.pdf]
11:15 – 11:45 Coffee Break
11:45 – 12:30 Lecture
Bottom-up Modelling: Systematic Coarse-Graining with VOTCA
Denis Andrienko (MPIP Mainz, Germany)
[talk.pdf]
12:30 – 14:00 Lunch break
14:00 – 17:30
Track 1: Hands-On
Membranes
Patrick Diggins (Carnegie-Mellon University, USA)
[worksheet.pdf] [mbtools.tar.gz]
Track 2: Hands-On
Two-Phase Flow
Marcello Sega (University of Vienna, Austria)
Track 3: Hands-On
Immersed Boundary Conditions
Iveta Jancingova, Renata Thotova (Faculty of Management Science and Informatics, University of Zilina, Slovakia)
[worksheet.pdf]
Track 4: Hands-On
Bottom-up-modelling with VOTCA
Victor Rühle (Cambridge University, UK), Christoph Junghans (Los Alamos National Laboratory, USA), Mara Jochum (Universität Mainz, Germany)
[Tutorial]
17:30 – Poster Session and BBQ

Wednesday, October 9th

9:00 – 10:30
Track 1: Lecture
Hydrodynamics in ESPResSo
Stefan Kesselheim (ICP Stuttgart, Germany)
[talk.pdf]
Track 2: Lecture
Recent and Future Developments of VOTCA
Christoph Junghans (Los Alamos National Laboratory, USA)
[talk.pdf]
10:30 – 11:00 Coffee Break
11:00 – 12:30
Track 1: Lecture
Electrostatics in ESPResSo
Axel Arnold, Florian Fahrenberger (ICP Stuttgart, Germany)
[talk-1.pdf] [talk-2.pdf]
Track 2: User Talks
Applications of VOTCA

  • Transferable coarse-grained force field for modeling of crystallization in alkanes
    Valentina Erastova (Durham University, UK)
    [talk.pdf]
  • Coarse-graining using the relative entropy method in VOTCA
    Sikandar Mashayak (University of Illinois at Urbana-Champaign, USA)
    [talk.pdf]
12:30 – 14:00 Lunch break
14:00 – 17:30
Track 1: Hands-On
Hydrodynamics in ESPResSo
Stefan Kesselheim (ICP Stuttgart, Germany)
[worksheet.pdf]
Track 2: Hands-On
Electrostatics in ESPResSo
Axel Arnold, Florian Fahrenberger, Florian Weik (ICP Stuttgart, Germany)
[worksheet.pdf] [tutorial.tar.gz]
Track 3: Hands-On
Advanced Coarse-Graining with VOTCA
Victor Rühle (Cambridge University, UK), Christoph Junghans (Los Alamos National Laboratory, USA)
[Tutorial]
17:30 – Conference Dinner

Thursday, October 10th

9:00 – 10:30
Track 1: Lecture
Rare Event Sampling
Kai Kratzer (ICP Stuttgart, Germany)
[Homepage]
Track 2: Lecture
ESPResSo++ and (H-)ADResS
Raffaello Potestio, Torsten Stühn (MPIP Mainz, Germany)
[talk.pdf]
10:30 – 11:00 Coffee Break
11:00 – 12:30
Track 1: Lecture
Recent and Future Developments of ESPResSo
Olaf Lenz, Marcello Sega, Markus Gusenbauer
[talk.pdf]
Track 2: Lecture
Computing Free Energies with PLUMED
Davide Branduardi (Max-Planck-Institute for Biophysics Frankfurt, Germany)
[talk.pdf]
12:30 – 14:00 Lunch break
14:00 – 17:30
Track 1: Hands-On
Rare Event Sampling
Kai Kratzer (ICP Stuttgart, Germany)
[worksheet.pdf]
Track 2: Hands-On
Computing Free Energies with PLUMED
Davide Branduardi (Max-Planck-Institute for Biophysics Frankfurt, Germany)
[talk.pdf] [worksheet.pdf]
Track 3: Hands-On
ESPResSo++ and (H-)ADResS
Karsten Kreis (MPIP Mainz, Germany)
[worksheet.pdf]

Friday, October 11th (Scientific Talks)

9:00 – 9:30 Transferable Coarse-grained Potential for Quantitative Protein Folding and Design
Ivan Coluzza (University of Vienna, Austria)
[talk.pdf]
9:30 – 10:00 Multiscale Methods for Complex Systems using AdresS and VOTCA
Debashish Mukherji (MPIP Mainz, Germany)
[talk.pdf]
10:00 – 10:30 Coffee Break
10:30 – 11:00 Obtaining the Bending Modulus from a Buckled Lipid Membrane
Patrick Diggins (Carnegie-Mellon-University Pittsburgh, USA)
[talk.pdf]
11:00 – 11:30 Crystallization of Charged Colloids ‒ when Hydrodynamics Matter
Axel Arnold (ICP Stuttgart, Germany)
[talk.pdf]
11:30 – 12:00 Wrap-up
Olaf Lenz, Axel Arnold, Christian Holm (ICP, Germany)
[worksheet.pdf]
Participants and Speakers of the ESPResSo Summer School 2013.

Participants and Speakers of the ESPResSo Summer School 2013.

Speakers

  1. Axel Arnold, Institute for Computational Physics, Stuttgart University,
    Germany
  2. Christian Holm, Institute for Computational Physics, Stuttgart University, Germany
  3. Stefan Kesselheim, Institute for Computational Physics, Stuttgart University, Germany
  4. Kai Kratzer, Institute for Computational Physics, Stuttgart University, Germany
  5. Olaf Lenz, Institute for Computational Physics, Stuttgart University, Germany
  6. Torsten Stühn, Max-Planck-Institute for Polymer Research, Mainz, Germany
  7. Debashish Mukherji, Max-Planck-Institute for Polymer Research, Mainz, Germany
  8. Vitaliy Starchenko, Max-Planck-Institute for Polymer Research, Mainz, Germany
  9. Denis Andrienko, Max-Planck-Institute for Polymer Research, Mainz, Germany
  10. Karsten Kreis, Max-Planck-Institute for Polymer Research, Mainz, Germany
  11. Raffaello Potestio, Max-Planck-Institute for Polymer Research, Mainz, Germany
  12. Davide Branduardi, Max-Planck-Institut for Biophysics, Frankfurt am Main, Germany
  13. Patrick Diggins, Carnegie-Mellon University, Pittsburgh, USA
  14. Ivan Coluzza, University of Vienna, Austria
  15. Markus Gusenbauer, Fachhochschule St. Pölten, Austria
  16. Iveta Jancigova, University of Zilina, Slovakia
  17. Renata Tothova, University of Zilina, Slovakia
  18. Christoph Junghans, Los Alamos National Laboratory, USA
  19. Sikandar Mashayak, Urbana, IL, USA
  20. Valentina Erastova
  21. Victor Rühle, Cambridge University, UK
  22. Marcello Sega, University of Vienna, Austria

Participants

  1. Florian Fahrenberger, Stuttgart University, Germany
  2. April Cooper, Stuttgart University, Germany
  3. Sascha Ehrhardt, Stuttgart University, Germany
  4. Jonas Landsgesell, Stuttgart University, Germany
  5. Patrick Kreissl, Stuttgart University, Germany
  6. Julian Michalowsky, Stuttgart University, Germany
  7. Gabriel Sichardt, Stuttgart University, Germany
  8. Kai Szuttor, Stuttgart University, Germany
  9. Michael Kuron, Stuttgart University, Germany
  10. Sebastian Weber, Stuttgart University, Germany
  11. Johannes Zeman, Stuttgart University, Germany
  12. Domenico Alberga, Bari, Italy
  13. Ibrahim Hamadan Allehyani, Riyadh, Saudi-Arabia
  14. Astrid Brandner, Montevideo, Uruguay
  15. Gabriel I Canto Santana, Campeche, Mexico
  16. Aviel Chaimovich, Mainz, Germany
  17. Vera Forster, Bayreuth, Germany
  18. Surya Ghosh, Potsdam, Germany
  19. Anton Iakovlev, Göttingen, Germany
  20. Jae-Hyung Jeon, Tampere, Finland
  21. Bin Li, Darmstadt, Germany
  22. Hector Martinez-Seara, Tampere, Finland
  23. Franksika Müller, Mainz, Germany
  24. Alexander Ryzhkov, Perm, Russia
  25. Jaeoh Shin, Potsdam, Germany
  26. Lucie Sucha, Prague, Czech Republic
  27. Hui-Chung Tai, Seoul, South Korea
  28. Luca Tubiana, Ljubljana, Slovenia
  29. Vincent Ustach, Davis, CA, USA
  30. Tetjana Vlaseko, Kyiv, Ukraine
  31. Wang Xiu, Prague, Czech Republic
  32. Ren Zhang, Darmstadt, Germany