Spring School in Computational Chemistry 2018 @ CSC

Europe/Helsinki
Training room Dogmi, 1st floor (CSC - IT Center for Science)

Training room Dogmi, 1st floor

CSC - IT Center for Science

Life Science Center, Keilaranta 14, Espoo, Finland
Description

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

    • 09:00 09:30
      Welcome and Introduction Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Dr. Atte Sillanpää

    • 09:30 10:00
      Introduction to Classical MD CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Luca Monticelli

    • 10:00 10:15
      Coffee break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 10:15 11:00
      Introduction to Classical MD: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Luca Monticelli

    • 11:00 11:15
      Break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 11:15 12:00
      Introduction to Classical MD: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Luca Monticelli

    • 12:00 13:00
      Lunch 1h Restaurant, Life Science Center Keilaniemi

      Restaurant, Life Science Center Keilaniemi

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 13:00 13:15
      Using CSC's environment - Pitching each tutorial CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Atte Sillanpää

    • 13:15 14:30
      MD workshop (advanced) TBA ()

      TBA

      Lecturer: Dr. Martti Louhivuori

    • 13:15 14:30
      MD workshop (basics) TBA ()

      TBA

      Lecturer: Dr. Atte Sillanpää

    • 13:15 14:30
      MD workshop (intermediate) TBA ()

      TBA

      Lecturer: Dr. Luca Monticelli

    • 14:30 15:00
      Coffee break 30m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 15:00 16:30
      MD workshop (advanced) TBA ()

      TBA

      Lecturer: Dr. Martti Louhivuori

    • 15:00 16:30
      MD workshop (intermediate) TBA ()

      TBA

      Lecturer: Dr. Luca Monticelli

    • 15:00 16:30
      MD-workshop (basics) TBA ()

      TBA

      Lecturer: Dr. Atte Sillanpää

    • 16:30 16:45
      Break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 16:45 17:30
      Accelerated Sampling Techniques CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Luca Monticelli

    • 17:30 19:00
      Poster session CSC's training lobby ()

      CSC's training lobby

    • 09:00 10:00
      Introduction to electronic-structure theory CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Mikael Johansson

    • 10:00 10:15
      Coffee break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

    • 10:15 11:00
      Introduction to electronic-structure theory: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Mikael Johansson

    • 11:00 11:15
      Break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 11:15 12:00
      Introduction to electronic-structure theory: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Mikael Johansson

    • 12:00 13:00
      Lunch 1h Restaurant, Life Science Center Keilaniemi

      Restaurant, Life Science Center Keilaniemi

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 13:00 14:30
      QC workshop (advanced) TBA ()

      TBA

      Life Science Center, Keilaranta 14, Espoo, Finland

      Lecturer: Dr. Mikael Johansson

    • 13:00 14:30
      QC workshop (basics) TBA ()

      TBA

      Life Science Center, Keilaranta 14, Espoo, Finland

      Lecturer: Dr. Michael Patzschke

    • 13:00 14:30
      QC workshop (intermediate) TBA ()

      TBA

      Life Science Center, Keilaranta 14, Espoo, Finland

      Lecturer: Dr. Nino Runeberg

    • 14:30 15:00
      Coffee break 30m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 15:00 16:45
      QC workshop (advanced) TBA ()

      TBA

      Lecturer: Dr. Mikael Johansson

    • 15:00 16:45
      QC workshop (basics) TBA ()

      TBA

      Lecturer: Dr. Michael Patzschke

    • 15:00 16:45
      QC workshop (intermediate) TBA ()

      TBA

      Lecturer: Dr. Nino Runeberg

    • 16:45 17:15
      Wrap up Discussion Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 09:00 10:00
      Machine Learning in Chemistry CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturers: Dr. Filippo Federici Canova, Yashasvi Ranawat

    • 10:00 10:15
      Coffee break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 10:15 11:00
      Machine Learning in Chemistry: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturers: Dr. Filippo Federici Canova, Yashasvi Ranawat

    • 11:00 11:15
      Break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 11:15 12:00
      Machine Learning in Chemistry: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturers: Dr. Filippo Federici Canova, Yashasvi Ranawat

    • 12:00 13:00
      Lunch 1h Restaurant, Life Science Center Keilaniemi

      Restaurant, Life Science Center Keilaniemi

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 13:00 13:45
      NOMAD introduction CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Dr. Atte Sillanpää

    • 13:45 14:00
      Coffee break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 14:00 15:00
      Visualizing your results. An introduction to VMD Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland

      Lecturer: Dr. Michael Patzschke

    • 15:00 15:15
      Coffee break 15m Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 15:15 16:30
      Visualizing your results. An introduction to VMD: continued Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Lecturer: Dr. Michael Patzschke

    • 16:30 17:00
      Break and transition 30m Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland

      Transition from training room Dogmi to A-building premises

    • 17:00 17:45
      Nuclear waste issues Life Science Center Keilaniemi, A-building, sauna department ()

      Life Science Center Keilaniemi, A-building, sauna department

      Lecturer: Dr. Michael Patzschke

    • 17:45 20:15
      Sauna evening & dinner 2h 30m Life Science Center Keilaniemi, A-building, sauna ()

      Life Science Center Keilaniemi, A-building, sauna

    • 09:00 10:00
      QMMM CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Prof. Ville Kaila

    • 10:00 10:15
      Coffee break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 10:15 11:00
      QMMM: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Prof. Ville Kaila

    • 11:00 11:15
      Break 15m CSC's training lobby

      CSC's training lobby

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 11:15 12:00
      QMMM: continued CSC's training room Dogmi ()

      CSC's training room Dogmi

      Lecturer: Prof. Ville Kaila

    • 12:00 13:00
      Lunch 1h Restaurant, Life Science Center Keilaniemi

      Restaurant, Life Science Center Keilaniemi

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland
    • 13:00 13:30
      HPC-Europa3 CSC's training room Dogmi ()

      CSC's training room Dogmi

      Dr. Atte Sillanpää

    • 13:30 15:00
      Analysing the wave function Training room Dogmi, 1st floor

      Training room Dogmi, 1st floor

      CSC - IT Center for Science

      Life Science Center, Keilaranta 14, Espoo, Finland

      Lecturer: Dr. Michael Patzschke

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