Caput College "Molecular modeling of crystal structures"
Course dates for 2004
(date [talk number])
9/9 [1], 16/9 [2], 23/9 [3], 30/9 [4];
7/10 [5], 14/10 [6].
Time: 13:45 - 15:30
Location: room N3058
Lectures (with links to powerpoint slides):
0: A short introduction
to unix (no presentation, only web material)
1: energy functions
2: modeling of small systems
(power point file uses this MD movie)
3: crystals
4: modeling of 3D-periodic systems
5: integration with experimental methods:
modeling of epitaxial growth, structure solution from powder data
by modeling
(power point file uses these MD movies:
md-450-1a.mpg,
md-450-1b.mpg,
md-450-1c.mpg,
md-450-2a.mpg,
md-450-2b.mpg,
md-450-4.mpg
)
6: QM and semi-empirical methods;
methods for visualization.
Speaker: Gijs Schaftenaar
Hands-on part
In addition to the talks, there is a hands-on course, available via the web
at
www.vsc.sci.kun.nl/verwer/cerius.
This one week computer practical is based on Accelrys's
Cerius2 software.
Contact person:
Paul Verwer
N3072, tel 53365, verwer@sci.kun.nl
Topics covered in this course:
- Modeling -- general
- thermodynamics
what is calculated?
- force fields
Functional form, parametrization, energy/geometry, 'consistent'
vs. 'physical', accuracy
- electrostatics
Mulliken, ESP, RESP. Multiple conformations
- Quantum mechanical and semi-empirical methods
- MD and MC
- Modeling 3D periodic structures
- technical complications
- cut-off radii; charge groups
- Ewald summation
- Attachment energy
- Modeling surfaces
- Prediction of crystal structures
- current approaches
- available software
- compound-specific considerations (SPGR, Z')
Spacegroup statistics, Z' statistics, chirality
- clustering
- Diffraction
- single crystals
- powder
- Rietveld refinement
- Using experimental information
- Software
- Molden
- Cerius
- UPACK
- crystallographic software
- plotting