MolSim 2017: Understanding Molecular Simulation
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In January 2017, the school MolSim2017 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-2017 is organized by the Amsterdam Center for Multiscale Modelling. Lecturers will include Daan Frenkel (Cambridge University), Berend Smit (EPFL Lausanne and Berkeley University), and Veronique van Speybroeck (Ghent University).
- Who: ACMM (Amsterdam Center for Multiscale Modeling)
- Where: University of Amsterdam
- When: January 9-20, 2017
- General information: visit the CECAM website by clicking this line.
Molsim-2017 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 MolSim-2017 school.
Day |
Hour |
Room |
Lecturer |
Course |
|
| Monday 9/1 | 08:30-09:00 | Main Hall | Registration | ||
| 09:10-09:15 | C0.110 | Evert Jan Meijer | Welcome | ||
| 09:15-12:30 | C0.110 | Berend Smit | Intro Statistical Thermodynamics part1part2 | ||
| 13:30-16:00 | A1.04, A1.10 | Lab Course | |||
| 16:00 | Welcome drinks | ||||
| Tuesday 10/1 | 09:00-12:30 | C0.110 | Berend Smit | Intro Monte Carlo | |
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Wednesday 11/1 | 09:00-12:30 | C0.110 | Berend Smit | Intro Molecular Dynamics | |
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Thursday 12/1 | 09:00-12:30 | C0.110 | Evert Jan Meijer | Ensembles | |
| 13:30-17:00 | A1.04, A1.10 | Lab Course | |||
| 17:00-20:00 | POSTER SESSION, DRINKS AND FOOD | ||||
| Friday 13/1 | 09:00-12:30 | C0.110 | Daan Frenkel | Monte Carlo: Advanced Methods I | |
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Saturday 14/1 | Day Off | ||||
| Sunday 15/1 | 16:00 | Social Event + Dinner | |||
| Monday 16/1 | 09:00-12:30 | C0.110 | Peter Bolhuis | Rare Events (I) | |
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Tuesday 17/1 | 09:00-10:15 | C0.110 | Peter Bolhuis | Rare Events (II) | |
| 10:45-12:30 | C0.110 | Sanne Abeln | Biological Methods - Lattice Models | ||
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Wednesday 18/1 | 09:00-12:30 | C0.110 | Evert Jan Meijer | Free Energies and Phase Equilibria | |
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Thursday 19/1 | 09:00-12:30 | C0.110 | Thijs Vlugt | MC: Advanced Methods II | |
| 13:30-18:00 | A1.04, A1.10 | Lab Course | |||
| Friday 20/1 | 09:15-10:30 | C0.05 | Veronique van Speybroeck | Lecture: Modeling Nanoporous Materials | |
| 10:30-11:00 | Hall | Coffee | |||
| 11:00-12:00 | C0.05 | Veronique van Speybroeck | Seminar: First principle molecular dynamics simulations for complex chemical transformations in nanoporous materials | ||
| 12:00 | C0.05 | Closing |
MolSim2017 Exercises
Click here to download the MolSim2017 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 or on a linux desktop computer, 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 molsim1@bazis.science.uva.nl:JohnAndJaneDoe_821/" (assuming that the account name is "molsim1"))
- 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 molsim1@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).
extra plot script
Click here to download a plot script "plot_q2" for exercise 4.4 question 2