MolSim-2019: Understanding Molecular Simulation
In January 2019, the school MolSim-2019 is scheduled to take place at the University of Amsterdam. The school hosts PhD and postdoc students working in the field of molecular simulation. MolSim-2019 is organized by the Amsterdam Center for Multiscale Modelling. Lecturers will include Daan Frenkel (Cambridge University), Berend Smit (EPFL Lausanne and Berkeley University), Ignacio Pagonabarraga (University of Barcelona and EPFL).
- Who: ACMM (Amsterdam Center for Multiscale Modeling)
- Where: University of Amsterdam
- When: January 7-18, 2019
Molsim-2019 Pictures
Pictures made during the school can be seen at
https://bit.ly/2RAKDkC
Molsim-2019 Program
The program consists of morning sessions with lectures, and afternoon sessions with hand-on exercises.
There will be a poster session, and during the weekend an organized social event.
Below you find the schedule of the school.
(Last update: Jan 24, 2019)
Day |
Hour |
Room |
Lecturer |
Course |
Lecture Notes |
| Monday 7/1 | 09:00-09:15 | C0.110 | Evert Jan Meijer | Welcome | |
| 09:15-12:00 | C0.110 | Berend Smit | Intro General | ||
| Intro Stat Mech | |||||
| 13:00-16:30 | G.010, G0.23 | Bernd Ensing David Dubbeldam | Lab Course | ||
| 16:30 | Welcome drinks | ||||
| Tuesday 8/1 | 09:00-12:00 | C0.110 | Berend Smit | Intro Monte Carlo |
|
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Wednesday 9/1 | 09:00-12:00 | C0.110 | Berend Smit | Intro Molecular Dynamics |
|
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Thursday 10/1 | 09:00-12:00 | C0.110 | Daan Frenkel | Advanced MC | |
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| 17:00-20:00 | Poster Session, Drinks and Food | ||||
| Friday 11/1 | 09:00-12:00 | C0.110 | Peter Bolhuis | Rare Events | |
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Saturday 12/1 | Day Off | ||||
| Sunday 13/1 | 16:00 | Social Event + Dinner | |||
| Monday 14/1 | 09:00-12:00 | C0.110 | Thijs Vlugt | MC - CBMC |
|
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Tuesday 15/1 | 09:00-12:00 | C0.110 | Evert Jan Meijer | Free Energies and Phase Equilibria |
|
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Wednesday 16/1 | 09:00-10:00 | C0.110 | Peter Bolhuis | Advanced MD | |
| 10:30-12:00 | C0.110 | Sanne Abeln | Biological Systems - Lattice Models (large file) | ||
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Thursday 17/1 | 09:00-10:30 | C0.110 | Leopold Talirz, Sasha Yakutovich, Dianne Ortega | Advanced: Computational Screening I - AiiDA Intro |
|
| II - Methane Storage | |||||
| 11:00-12:00 | G3.02, G0.23 | Leopold Talirz, Sasha Yakutovich, Danielle Ongari | Lab Course | ||
| 13:00-17:00 | G0.10, G0.23 | Lab Course | |||
| Friday 18/1 | 09:30-10:30 | C0.110 | Ignacio Pagonabarraga | Introductory Lecture | |
| 11:00-12:00 | C0.110 | Ignacio Pagonabarraga | Research Seminar | ||
| 12:00 | C0.110 | Peter Bolhuis | Closing |
Affiliations Lecturers:
Ignacio Pagonabarraga - EPFL, CECAM, University of Barcelona
Sanne Abeln - Free University Amsterdam
Thijs Vlugt - Delft University of Technology
Daan Frenkel - University of Cambridge
Berend Smit - EPFL and University of California Berkeley
Leopold Talirz - EPFL
Sasha Yakutovich - EPFL
Daniele Ongari - EPFL
Bernd Ensing - University of Amsterdam
David Dubbeldam - University of Amsterdam
Peter Bolhuis - University of Amsterdam
Evert Jan Meijer - University of Amsterdam
MolSim-2019 Exercises
Click here to download the MolSim2019 exercises
- choose "save file"
- depending on your situation, choose between these
options:
- OPTION 1: if you will compile and run the exercises on your own laptop, create a directory (e.g. "molsim") and move the downloaded "Exercises.tar.gz" file in this directory.
- OPTION 2: if you will compile and run the exercises remotely on the Bazis computer, make a unique directory (e.g. "JohnAndJaneDoe_821") on the Bazis cluster and move the downloaded "Exercises.tar.gz" file in this directory (e.g. open a terminal and execute the command: "scp ~/Downloads/Exercises.tar.gz molsimxx@bazis.science.uva.nl:JohnAndJaneDoe_821/" (assuming that the account name is "molsimxx"))
- open a terminal window
- change directory to the one that you created and moved the "Exercises.tar.gz" file to (e.g. "cd ~/molsim"); if you moved it to the Bazis computer, first login to that machine (e.g. "ssh molsimxx@bazis.science.uva.nl").
- unpack the file "Exercises.tar.gz" by typing the unix command "tar -xzvf Exercises.tar.gz"
- now you should have a directory "Exercises" in your home-directory (assuming that the file "Exercises.tar.gz" was saved in the directory that you are currently in).
Click here to
download the extra Rare Event exercise on metadynamics
MolSim exercises on Windows-10
Click here to download the guide for doing the Molsim labcourse on a Windows10 computer
The guide provides a step-by-step instructions to install a linux environment (virtual machine) on your Windows10 computer, together with an X-server that is used to draw graphics windows.
Install Quantum Mobile; preparation for Thursday Session (Jan 17)
Click on the following link to install quantum mobile: www.materialscloud.org/work/quantum-mobile
The guide provides a step-by-step instructions to install a linux environment (virtual machine) and the quantum mobile environment.
The link to install the virtual environment on your local machine: LINK