Lectures

GENESIS Tutorial in Tsukuba or online [Sep. 28, 2021]

GENESIS Hands-on tutorial will be held at Tsukuba University or online using BlueJeans. We will demonstrate how to execute GENESIS on the supercomputer Cygnus in Tsukuba University. For details see the HPCI website (in Japanese).

Speakers: Chigusa Kobayashi, Daisuke Matsuoka (RIST), Osamu Takebe (Tsukuba U.)

  • Overview of GENESIS (Slides)
  • Introduction of the supercomputer Cygnus
  • Hans-on tutorial or demonstration using GENESIS (Slides) (including answers of questions in meeting)
GENESIS Tutorial in Tsukuba or online [Jan. 29, 2021]

GENESIS Hands-on tutorial will be held at Tsukuba University or online using BlueJeans. We will demonstrate how to execute GENESIS on the supercomputer Cygnus in Tsukuba University. For details see the HPCI website (in Japanese).

Speakers: Chigusa Kobayashi, Jaewoon Jung, Daisuke Matsuoka (RIST), Osamu Takebe (Tsukuba U.)

  • Overview of GENESIS (Slides)
  • Introduction of the supercomputer Cygnus
  • Hans-on tutorial or demonstration using GENESIS (Slides)
GENESIS Tutorial online [Oct. 29, 2020]

This tutorial was held in the CBI Annual Meeting 2020. In the session, we showed demonstration movies of the free energy purturbation (FEP) and cryo-EM flexible fitting implemented in GENESIS (Session abstract in Japanese). The movie will be available soon in YouTube.

Speakers: Suyong Re, Hiraku Oshima, and Takaharu Mori

  • Opening remarks: Overview of GENESIS
  • Demonstration 1: Free energy calculation for protein-ligand binding
  • Demonstration 2: Cryo-EM flexible fitting
GENESIS Tutorial in Poland [Nov. 20-21, 2019]

This hands-on tutorial (joint tutorial with RedMDStream and MINT) was held in the “Workshop on molecular dynamics based binding free energy calculations, post-processing of trajectories and force field development” at University of Warsaw in Poland.

Speakers: Yuji Sugita, Jaewoon Jung, Chigusa Kobayashi, Suyong Re, and Takaharu Mori

  • Lecture: Overview of GENESIS
  • Lecture: General introduction of MD & Performance optimization of GENESIS
  • Tutorial: Quick start of GENESIS
  • Lecture: An application of GENESIS: Simulating protein-ligand bindings
  • Tutorial: Modeling complex biological systems
GENESIS Tutorial in Tokyo [Oct. 5, 2017]

This hands-on tutorial was held in the CBI Annual Meeting 2017 (Announcement).

Speakers: Yuji Sugita, Chigusa Kobayashi, and Motoshi Kamiya

  • Lecture: GENESIS overview (Japanese) (Slides)
  • Tutorial 1: Basic usage of GENESIS (Japanese) (Slides, Materials)
  • Tutorial 2: Free energy calculation methods in GENESIS (Japanese) (Slides, Materials)
GENESIS Tutorial in Kobe [Feb. 27-Mar. 1, 2017]

This hans-on tutorial was held in the International Workshop “Frontiers in Computational Biophysics and Biochemistry”.

Speakers: Chigusa Kobayashi, Jaewoon Jung, Takaharu Mori, and Yasuhiro Matsunaga

AICS Software “GENESIS” Hands-On Tutorial [Jan. 11, 2017]
GENESIS Lecture for Post-K Priority Issue 01 [Sep. 7, 2016]
AICS Software “GENESIS” Hands-On Tutorial [Sep. 4, 2015]
AICS Software “GENESIS” Hands-On Tutorial [Jun. 17, 2014]