53363 Molecular Dynamics Simulations (10 ECTS) autumn 2013

The exam takes place on Wednesday, 11.12. from 10:00 to 14:00 in Physicum D106!

This course is a 10 ECTS credit points course on atomistic simulations. We will concentrate on molecular dynamics simulations (MD) which enable following the evolution of a system of point-like objects over time. During the course, students will write in a supervised manner their own MD code which can be used to model atomic motion in simple metals. Simulations of fluids will be performed with the GROMACS code. The course will also cover some energy minimization methods as well as the nudged elastic band (NEB) method for migration energy barrier calculations. Quantum mechanical and classical atomic interaction models will be covered, main stress being on classical methods. Visualization and analysis methods of atomic data are also discussed. Some knowledge of programming will be immensely helpful during the course, preferably in Unix/Linux environment. In addition, the students should have the basic knowledge of thermodynamics and statistical physics. The course is a part of the MoMoNano Master's programme.

The exam takes place on Wednesday, 11.12. from 10:00 to 14:00 in Physicum D106!

General information

Exam on Wednesday, 11.12. from 10:00 to 14:00 in Physicum D106
lectures on Wednesdays in Physicum D114 at 10:15 - 12:00 - the course is lectured in English
exercise sessions on Fridays in Physicum D115 at 11.15-12.00 --- please note the changed time! Now you have time to attend Kumpula Computational Chemistry and Physics seminar!
lecturers: Johannes Niskanen and Henning Henschel
assistant: Ville Loukonen

Lectures

Lecture 01 (04.09.) [.pdf]
- practicalities
- overview of MD
Lecture 02 (11.09.) [.pdf]
- fundamental principles of MD
- setting up a simulation
Lecture 03 (18.09.) [.pdf]
- neighbourlists
- solving the equations of motion
Lecture 04 (25.9.) [.pdf]
- interaction potentials
- calculating forces
Lecture 05 (2.10.) [.pdf]
- controlling temperature, controlling pressure, controlling temperature and pressure
Lecture 06 (9.10.) [.pdf]
- Estimating errors
- Minimization methods
Lecture 07 (16.10.) [.pdf]
- Ab Initio MD
Lecture 08 (30.10.) [.pdf]
- Ionic Interactions
Lecture 09 (06.11.) [.pdf]
- Molecular Mechanics
- Free Energy Calculations
Lecture 10 (13.11.) [.pdf]
- Interaction Models for Metals
Lecture 11 (20.11.) [.pdf]
- Interaction Models for Covalent Materials
Lecture 12 (27.11.) [.pdf]
- Path Optimisation Methods

Exercises

Exercise 01 [.pdf] - return by 11.09.
- the mystery.xyz
Exercise 02 [.pdf] - return by 18.09.
- the mystery.xyz - note that mystery.xyz has the box dimensions as the first 3 numbers on the comment line
Exercise 03 [.pdf] - return by very latest before the session on Friday 27.09.
- the mystery.xyz
Exercise 04 [.pdf] - return by very latest before the session on Friday 4.10.
- the Exc4.files.tar.gz - if you have any difficulties with computers or running the simulations, Johannes will try to help
Exercise 05 [.pdf] - return by very latest before the session on Friday 11.10.
Exercise 06 [.pdf] - return by very latest before the session on Friday 18.10.
- for assignment 2: Exc6.a2.files.tar.gz
- In addition, for sample .mdp files e6.a1.NVE.mdp, e6.a2.bere.mdp and e6.a2.nose.mdp
Exercise 07 [.pdf] - return by very latest before the session on Friday 01.11.
- Ex7.tar.gz
Exercise 08 [.pdf] - return into the box during Thursday afternoon, or by very latest, in the session on Friday 08.11.
- NVT115ber.mdp, a sample NVT(T=115K) with Berendsen simulation parameter file
- NVT115ber.gro, a sample .gro file for this particular system
- NVT115ber.trr, a sample .trr file for this particular system
- NVE115.mdp, a sample NVE simulation parameter file (to be used with NVTber115.gro and .trr files)
- NVT115nh.mdp, a sample NVT(T=115K) with Nosé-Hoover simulation parameter file
- ar.top, a sample topology file for LJ argon with 1000 atoms
Exercise 09 [.pdf] - return into the box during Thursday afternoon, or by very latest, in the session on Friday 15.11.
- Ex9.tar.gz
Exercise 10 [.pdf] - return into the box during Thursday afternoon, or by very latest, in the session on Friday 22.11.
- Ex10.tar.gz
Exercise 11 [.pdf] - return into the box during Thursday afternoon, or by very latest, in the session on Friday 29.11. --- this was the last exercise session of course!

Please give anonymous feedback for the first 6 weeks of the course here . For our improvement it is vital to get your comments. This query was also prepared to be very short to not take much of your time.

Due to feedback already obtained, some sample input files for excercise 6 were added. Thanks to those who already gave feedback!

Presentations

15 minutes in the beginning of the lecture. Please be there around 10.00 so we have time to set things up.
If you do not still have time or title (and will give a talk instead of an essay), contact Johannes. We can figure out more works.

date	name	topic
18.09.	Junlei	MD simulations on Ag induced crystallization in Si Nanoclusters
25.09.	Morten	TBA (own research)
02.10.	-	-
09.10.	Bartosz	MD of biomolecules
16.10.	Fabian	MD for protein folding
23.10.	mid-term break	no lecture
30.10.	Mehdi	MC simulation of binary gas flow
06.11.	Ville	TBA (own research)
13.11.	Ekaterina	MD for large systems
20.11.	Roope	Early MD
27.11.	Hakan	MD using quaternions
04.12.
11.12.

Additional material

The lectures do not follow any particular book. However, there exists several books on molecular dynamics. For example, the following might be interesting:

Allen and Tildeslay, Computer Simulation of Liquids, Oxford University Press (1987)
Leach, Molecular Modelling: Principles and Applications, Prentice Hall (2001)
Frenkel and Smit, Understanding Molecular Simulation, Academic Press (2001)
Haile, Molecular Dynamics Simulation: Elementary Methods, Wiley Professional (1997)
Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford University Press (2010)
Marx and Hutter, Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods, Cambridge University Press (2009)

Also, around the internet there exists several lecture notes from other molecular dynamics courses. For example:

Molecular Simulations and Advanced Molecular Simulations (by Wei Cai, Stanford University)
A molecular dynamics primer (by Furio Ercolessi, University of Udine)
Molecular Dynamics I (video, .pdf), II (video, .pdf), III (video, .pdf by Nicola Marzari, MIT)
this course 2012, 2011, 2010, 2008.

Fast, flexible and free molecular dynamics simulation code GROMACS can be found and downloaded from here. If you happen to be using Ubuntu, GROMACS can even be installed directly from the Ubuntu Software Centre. Unlike many other simulation software, GROMACS comes with a great manual!