MolSim-2020: Understanding Molecular Simulation

In January 2020, the school MolSim-2020 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-2018 is organized by the Amsterdam Center for Multiscale Modeling.

Molsim-2020 Pictures

Pictures made during the school will follow.

Molsim-2020 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.






Lecture Notes

Monday 6/1 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 David Dubbeldam Bernd Ensing Lab Course
16:30 Welcome drinks
Tuesday 7/1 09:00-12:00C0.110 Berend Smit Intro Monte Carlo
13:00-17:00G0.10, G0.23 Lab Course
Wednesday 8/1 09:00-12:00C0.110 Berend Smit Intro Molecular Dynamics
13:00-17:00G0.10, G0.23 Lab Course
Thursday 9/1 09:00-12:00C0.110 Thijs Vlugt MC - CBMC
13:00-17:00G0.10, G0.23 Lab Course
09:00-12:00C0.110 Evert Jan Meijer Ensembles

Free Energies and Phase Equilibria
13:00-17:00G0.10, G0.23 Lab Course
Saturday 11/1 Day Off
Sunday 12/1 16:00Social Event + Dinner
Monday 13/1 09:00-12:00C0.110 Daan Frenkel MC - Advanced
13:00-17:00G0.10, G0.23 Lab Course
Tuesday 14/1 09:00-10:30C0.110 Tristan Bereau Machine Learning - I
11:00-12:15C0.110Sanne Abeln Biological Systems
powerpoint (small)
pdf (large)
13:00-17:00G0.10, G0.23 Lab Course
Wednesday 15/1 09:00-12:00C0.110 Peter Bolhuis Rare Events
13:00-17:00G0.10, G0.23 Lab Course
Thursday 16/1 09:00-12:00C0.110 Mohamad Moosavi/Kevin Jablonka Machine Learning - II
13:00-17:00G0.10, G0.23Kevin Jablonka/Mohamad Moosavi Lab Course
Friday 17/1 09:30-10:30C0.110 Nicola Marzari Why is DFT like Tinder?
11:00-12:00C0.110 Nicola Marzari The great acceleration in materials discovery
~12:00C0.110Evert Jan Meijer Closing

Affiliations Lecturers:
Nicola Marzari - EPFL
Tristan Bereau - University of Amsterdam and MPI Polymer Research
Mohamad Moosavi - EPFL
Kevin Jablonka - EPFL
Sanne Abeln - Free University Amsterdam
Thijs Vlugt - Delft University of Technology
Daan Frenkel - University of Cambridge
Berend Smit - EPFL
Bernd Ensing - University of Amsterdam
David Dubbeldam - University of Amsterdam
Peter Bolhuis - University of Amsterdam
Evert Jan Meijer - University of Amsterdam

MolSim-2020 Exercises

Click here to download the MolSim2020 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 "molsimxx"))
  • open a terminal window
  • change directory to the one that you created and move 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 for 15 January.

Click here for the exercise session on machine learning on 16 January.