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).

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.






Monday 9/1 08:30-09:00Main Hall Registration
09:10-09:15C0.110Evert Jan Meijer Welcome
09:15-12:30C0.110Berend Smit Intro Statistical Thermodynamics part1part2
13:30-16:00A1.04, A1.10 Lab Course
16:00 Welcome drinks
Tuesday 10/1 09:00-12:30C0.110Berend Smit Intro Monte Carlo
13:30-18:00A1.04, A1.10 Lab Course
Wednesday 11/1 09:00-12:30C0.110Berend Smit Intro Molecular Dynamics
13:30-18:00A1.04, A1.10 Lab Course
Thursday 12/1 09:00-12:30C0.110Evert Jan Meijer Ensembles
13:30-17:00A1.04, A1.10 Lab Course
09:00-12:30C0.110Daan Frenkel Monte Carlo: Advanced Methods I
13:30-18:00A1.04, A1.10 Lab Course
Saturday 14/1 Day Off
Sunday 15/1 16:00 Social Event + Dinner
Monday 16/1 09:00-12:30C0.110Peter Bolhuis Rare Events (I)
13:30-18:00A1.04, A1.10 Lab Course
Tuesday 17/1 09:00-10:15C0.110Peter Bolhuis Rare Events (II)
10:45-12:30C0.110Sanne Abeln Biological Methods - Lattice Models
13:30-18:00A1.04, A1.10 Lab Course
Wednesday 18/1 09:00-12:30C0.110Evert Jan Meijer Free Energies and Phase Equilibria
13:30-18:00A1.04, A1.10 Lab Course
Thursday 19/1 09:00-12:30C0.110Thijs Vlugt MC: Advanced Methods II
13:30-18:00A1.04, A1.10 Lab Course
Friday 20/1 09:15-10:30C0.05Veronique van SpeybroeckLecture: Modeling Nanoporous Materials
11:00-12:00C0.05Veronique van Speybroeck Seminar: First principle molecular dynamics simulations for complex chemical transformations in nanoporous materials
12:00C0.05 Closing

MolSim2017 Exercises

Click here to download the MolSim2017 exercises

  • choose "save file"
  • depending on your situation, choose between these options:
    1. 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.
    2. 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" (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").
  • 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

new CFCMC excercise thursday 19 January

Click here to download the CFCMC excercise