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

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)






Lecture Notes

Monday 7/1 09:00-09:15C0.110Evert Jan Meijer Welcome
09:15-12:00C0.110 Berend Smit Intro General
Intro Stat Mech
13:00-16:30G.010, G0.23 Bernd Ensing David Dubbeldam Lab Course
16:30 Welcome drinks
Tuesday 8/1 09:00-12:00C0.110 Berend Smit Intro Monte Carlo
13:00-17:00G0.10, G0.23 Lab Course
Wednesday 9/1 09:00-12:00C0.110 Berend Smit Intro Molecular Dynamics
13:00-17:00G0.10, G0.23 Lab Course
Thursday 10/1 09:00-12:00C0.110 Daan Frenkel Advanced MC
13:00-17:00G0.10, G0.23 Lab Course
17:00-20:00 Poster Session, Drinks and Food
09:00-12:00C0.110 Peter Bolhuis Rare Events
13:00-17:00G0.10, G0.23 Lab Course
Saturday 12/1 Day Off
Sunday 13/1 16:00Social Event + Dinner
Monday 14/1 09:00-12:00C0.110 Thijs Vlugt MC - CBMC
13:00-17:00G0.10, G0.23 Lab Course
Tuesday 15/1 09:00-12:00C0.110 Evert Jan Meijer Free Energies and Phase Equilibria
13:00-17:00G0.10, G0.23 Lab Course
Wednesday 16/1 09:00-10:00C0.110 Peter Bolhuis Advanced MD
10:30-12:00C0.110Sanne Abeln Biological Systems - Lattice Models (large file)
13:00-17:00G0.10, G0.23 Lab Course
Thursday 17/1 09:00-10:30C0.110 Leopold Talirz, Sasha Yakutovich, Dianne Ortega Advanced: Computational Screening
I - AiiDA Intro
II - Methane Storage
11:00-12:00G3.02, G0.23Leopold Talirz, Sasha Yakutovich, Danielle Ongari Lab Course
13:00-17:00G0.10, G0.23 Lab Course
Friday 18/1 09:30-10:30C0.110 Ignacio Pagonabarraga Introductory Lecture
11:00-12:00C0.110 Ignacio PagonabarragaResearch Seminar
12:00C0.110Peter 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:
    1. 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.
    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 "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").
  • 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:
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