Description
The Spring School provides a comprehensive, tutorial-style, hands-on, introductory and intermediate-level treatment to the essential ingredients for molecular modeling and computational chemistry using modern supercomputers. The School program is being prepared, but the main content will be similar to last years and consists of:
- Classical molecular dynamics, intro + hands on (1 day)
- Electronic structure theory, intro + hands on (1 day)
- Machine learning in chemistry, intro + hands on
- Special topics: e.g. on QM/MM, Visualization, Enchanced Sampling Techniques, etc.
The school is a must for graduate students in the field, providing an overview on "what can be calculated and how should it be done", without forgetting the important aspect of network building.
Learning outcome
The learning outcome is to gain an overview of the two main methods in computational chemistry — molecular dynamics and electronic structure calculations — in connection with related HPC software packages and other useful skills in the trade. The workshop is also suited for an intensive crash course (the first two days) in computational modelling and is expected to be useful for students and researchers also in physics, materials sciences and biosciences. The following "Special topics" then build on this foundation.
Prerequisites
Working knowledge and some work experience from some branch of computational chemistry will be useful. Basic linux skills for hands-on exercises and elementary Python for Machine Learning hands-on. More detailed description of pre-requisites and links for self study.
Programme
See Timetable on the left menu or comments from participants in 2017.
Lecturers:
- Dr. Filippo Federici Canova, Aalto University, Finland
- Dr. Mikael Johansson, University of Helsinki, Finland
- Prof. Ville Kaila, Technical University of Munich, Germany
- Dr. Luca Monticelli, IBCP (CNRS), Lyon, France
- Dr. Michael Patzschke, Helmholtz-Zentrum Dresden-Rossendorf, Germany
- Yashasvi Ranawat, Aalto University, Finland
- Dr. Markus Koskela, CSC - IT Center for Science, Finland
- Dr. Martti Louhivuori, CSC - IT Center for Science, Finland
- Dr. Atte Sillanpää, CSC - IT Center for Science, Finland
- Dr. Nino Runeberg, CSC- IT Center for Science, Finland
Software used in the hands-on exercises
For MD
GROMACS 5.1.5 http://manual.gromacs.org/documentation/5.1.5/download.html
dssp 2.0.4 ftp://ftp.cmbi.ru.nl/pub/software/dssp/
grace ftp://plasma-gate.weizmann.ac.il/pub/grace/src/
For QC
ORCA 4.0.1.2 https://cec.mpg.de/orcadownload/index.php (Registration required)
Gabedit 250 https://sourceforge.net/projects/gabedit/files/gabedit/Gabedit250/
TmoleX 4.3 http://www.cosmologic.de/support-download/downloads/tmolex-client.html
NWChem 6.8 https://github.com/nwchemgit/nwchem/releases/tag/v6.8-release
Jmol-14.29.5 https://sourceforge.net/projects/jmol/files/latest/download?source=files
CubeDiff r97 http://isilanes.org/soft/cubediff/?sec=down
For Analyzing electron density
Molden 5.7 ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/molden5.7.tar.gz
molden2aim 4.2.0 https://github.com/zorkzou/Molden2AIM
NCIPLOT 3.0 http://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html
Multiwfn 3.4.1 http://sobereva.com/multiwfn/
JANPA 1.04 http://janpa.sourceforge.net/
mep.py https://gist.github.com/mretegan/5501553
For VMD
VMD 1.9.4a12 http://www.ks.uiuc.edu/Development/Download/download.cgi
Graphical access to CSC servers
NoMachine Enterprise client v 6.0 https://www.nomachine.com/download-enterprise
https://research.csc.fi/csc-guide-connecting-the-servers-of-csc#1.3.3
Language: English
Price: Free of charge
