MolSim-2018: Understanding Molecular Simulation

In January 2018, the school MolSim-2018 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 Modelling. Lecturers will include Daan Frenkel (Cambridge University), Berend Smit (EPFL Lausanne and Berkeley University), Gregory Voth (University of Chicago), and Rodolphe Vuilleumier (ENS Paris).

  • Who: ACMM (Amsterdam Center for Multiscale Modeling)
  • Where: University of Amsterdam
  • When: Two weeks in January 2018

Molsim-2018 Pictures

Pictures made during the school can be seen at

Molsim-2018 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 program of the school.






Lecture Notes

Monday 8/1 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 9/1 09:00-12:00C0.110 Berend Smit Intro Monte Carlo
13:00-17:00G0.10, G0.23 Lab Course
Wednesday 10/1 09:00-12:00C0.110 Berend Smit Intro Molecular Dynamics
13:00-17:00G0.10, G0.23 Lab Course
Thursday 11/1 09:00-12:00C0.110 Peter Bolhuis Advanced MD
13:00-17:00G0.10, G0.23 Lab Course
09:00-12:00C0.110 Evert Jan Meijer Free Energies and Phase Equilibria
13:00-17:00G0.10, G0.23 Lab Course
Saturday 13/1 Day Off
Sunday 14/1 16:00Social Event + Dinner
Monday 15/1 09:00-12:00C0.110 Thijs Vlugt MC - CBMC
13:00-17:00G0.10, G0.23 Lab Course
Tuesday 16/1 09:00-12:00C0.110 Daan Frenkel MC - Advanced Methods
13:00-17:00G0.10, G0.23 Lab Course
Wednesday 17/1 09:00-10:30C0.110 Gregory Voth Systematic Coarse-graining: Fundamentals and Applications Abstract
11:00-12:15C0.110Sanne Abeln Biological Systems - Lattice Models
13:00-17:00G0.10, G0.23 Lab Course
Thursday 18/1 09:00-12:00C0.110 Peter Bolhuis Rare Events
13:00-17:00G0.10, G0.23 Lab Course
Friday 19/1 09:30-10:30C0.110 Evert Jan Meijer Introduction to First Principles Molecular Dynamics
11:00-12:00C0.110 Rodolphe VuilleumierApplications of FPMD to Earth Sciences: From Hydrothermal Sources to the Earth Mantle
~11:30C0.110Evert Jan Meijer Closing

Affiliations Lecturers:
Gregory Voth - University of Chicago
Rodolphe Vuilleumier - ENS Paris
Sanne Abeln - Free University Amsterdam
Thijs Vlugt - Delft University of Technology
Daan Frenkel - University of Cambridge
Berend Smit - EPFL and University of California Berkeley
Bernd Ensing - University of Amsterdam
David Dubbeldam - University of Amsterdam
Peter Bolhuis - University of Amsterdam
Evert Jan Meijer - University of Amsterdam

MolSim-2018 Exercises

Click here to download the MolSim2018 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 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).

new CFCMC excercise monday 15 January

Click here to download the CFCMC excercise