MolSim 2016: Understanding Molecular Simulation

In January 2016, the school MolSim2016 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-2016 is organized by the Amsterdam Center for Multiscale Modelling. Lecturers will include Daan Frenkel (Cambridge University), Berend Smit (EPFL Lausanne and Berkeley University), and Ali Alavi (Cambridge University and MPI for Solid State Research).

Molsim-2016 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 general framework of the schedule of the MolSim-2016 school.






Monday 4/1 09:10-09:15C0.110 Welcome
09:15-12:30C0.110Berend SmitIntroduction
Intro Statistical Thermodynamics
13:30-16:00A1.04, D1.111 Lab Course
16:00 Welcome drinks
Tuesday 5/1 09:00-12:30C0.110Berend Smit Intro Monte Carlo
13:30-18:00A1.04, D1.111 Lab Course
Wednesday 6/1 09:00-12:30C0.110Berend Smit Intro Molecular Dynamics
13:30-18:00A1.04, D1.111 Lab Course
Thursday 7/1 09:00-12:30C0.110Evert Jan Meijer MC: Advanced Methods I
13:30-17:00A1.04, D1.111 Lab Course
09:00-12:30C0.110Thijs Vlugt Configurational Bias Monte Carlo
13:30-18:00A1.04, B1.24ABCD Lab Course
Saturday 9/1 Day Off
Sunday 10/1 16:00 Social Event + Dinner
Monday 11/1 09:00-12:30C0.110Evert Jan Meijer Free Energies and Phase Equilibria
13:30-18:00A1.04, B1.24ABCD Lab Course
Tuesday 12/1 09:00-12:30C0.110Peter Bolhuis Rare Events
13:30-18:00A1.04, D1.111 Lab Course
Wednesday 13/1 09:00-10:30C0.110Sara Bonella Advanced Methods: Quantum Effects
11:00-12:30C0.110Sanne Abeln Biological Methods - Lattice Models
13:30-18:00A1.04, D1.111 Lab Course
Thursday 14/1 09:00-12:30C0.110Daan Frenkel MC: Advanced Methods II
13:30-18:00A1.04, D1.111 Lab Course
Friday 15/1 09:00-10:00C0.110Ali AlaviLecture: MC in Electronic Structure Calculations
11:00-12:00C0.110Ali Alavi Seminar: MC in Electronic Structure Calculations
12:00C0.110 Closing

MolSim2016 Exercises

Click here to download the MolSim2016 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 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).