Lectures
IUPAB2024 Hands-on Training Program CHARMM-GUI/GENESIS MD Tutorial in Kobe [Jun. 30- Jul. 2, 2024]
This workshop was held as a IUPAB2024 Hands-on Training Program. For details see the page.
- GENESIS basics and GENESIS on Fugaku (Slide) (Speaker: Chigusa Kobayashi)
- Coarse-grained simulations in GENESIS (Slide) (Speaker: Cheng Tan)
- High-performance computation with GENESIS (Slide) (Speaker: Jaewoon Jung)
- Generalized-ensemble simulations using GENESIS (Slide) (Speaker: Shingo Ito)
(Slides of lecture parts are available.)
GENESIS Lecture in Nagoya University [May 20, 2024]
GENESIS Lecture was held at Nagoya University via onsite and online. For details see the page in information and communication of Nagoya University. (in Japanese)
Speaker: Chigusa Kobayashi (RIKEN)
GENESIS Summer School [Aug. 1-2, 2022]
GENESIS summer school will be held via online. For details see the page.
GENESIS Hands-on tutorial on Fugaku [May. 11, 2022]
GENESIS Hands-on tutorial on Fugaku was held via online. We demonstrated how to execute GENESIS on the supercomputer Fugaku in R-CCS. For details see the page in LINC (in Japanese).
Speaker: Chigusa Kobayashi (RIKEN)
- Overview of GENESIS (Slides)
- Hands-on tutorial on Fugaku
GENESIS Tutorial in Tsukuba or online [Sep. 28, 2021]
GENESIS Hands-on tutorial was held at Tsukuba University or online using BlueJeans. We demonstrated 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 was held at Tsukuba University or online using BlueJeans. We demonstrated 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
- Tutorial 1: Basic MD (Slides, Materials)
- Tutorial 2: Advanced MD (Slides, Materials)
- Tutorial 3: REMD (Slides, Materials)
- Tutorial 4: String Method (Slides, Materials)