IUPAB2024 Hands-on Training Program


June 30 (Sun.) – July 02 (Tue.), 2024

Integrated Innovation Building (IIB), RIKEN Kobe

6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Japan

General Information

Welcome to our comprehensive workshop on molecular dynamics simulations, hosted by the Computational Biophysics Research Team at R-CCS. This unique event is designed to offer both theoretical insights and practical skills in the field of computational modeling, specifically tailored for graduate students and experimentalists eager to jump into the dynamic world of biomolecules.
  • Date: June 30 (Sun.) – July 02 (Tue.), 2024
  • Location: the 8th floor, Integrated Innovation Building (IIB), RIKEN, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
  • Access: for details, please visit https://cbp.riken.jp/en/access/. The nearest station is Iryo Center via the Port Liner.

Workshop Overview

Objective: Our workshop serves two main purposes:
  1. To facilitate discussions on the recent advancements in computational biophysics research.
  2. To provide on-site, hands-on tutorials on CHARMM-GUI and GENESIS, enabling participants to apply these tools effectively in their research endeavors.

Program Structure

  • Morning Sessions: Dedicated to lectures on cutting-edge research in computational biophysics. These sessions aim to provide attendees with an understanding of current trends and methodologies in the field. Lectures will be accessible both on-site and online, ensuring wide participation.
  • Afternoon Sessions: Focused on hands-on tutorials using CHARMM-GUI and GENESIS. These sessions are designed to offer practical experience in building biomolecular systems for simulation (using CHARMM-GUI) and performing high-performance multi-scale molecular dynamics simulations (using GENESIS).
  • Fugaku Tour: Experience the cutting-edge of computing with the Fugaku Tour, an exclusive opportunity for external visitors to get an up-close look at the Fugaku Supercomputer.
Please note, the hands-on tutorials are available exclusively on-site. (The maximum capacity is 20 participants.) There are no limitations of online participants in the morning sessions.

Learning Outcomes

Participants will:
  • Have the opportunity to discuss their research interests with leading scholars in the field of computational biophysics, enhancing their understanding and application of computational tools in biomolecular studies. (from morning sessions)
  • Gain hands-on experience with CHARMM-GUI and GENESIS under the guidance of the Computational Biophysics Research Team. (from afternoon sessions)
  • Learn to build varied biomolecular systems and perform sophisticated molecular dynamics simulations. (from afternoon sessions)
We look forward to welcoming you to an engaging and informative experience, where theory meets practice in the exploration of molecular dynamics.  

Invited Speakers for Morning Sessions

  • Alberto Perez, University of Florida
  • Bernard Brooks, NIH
  • Ben Corry, Australian National University
  • Chen Song, Peking University
  • Florence Tama, RIKEN
  • Helmut Grubmüller, Max Planck Institute for Multidisciplinary Sciences
  • Gerhard Hummer, Max Planck Institute of Biophysics
  • Jana Shen, University of Maryland
  • Jianhan Chen, University of Massachusetts
  • Kei Moritsugu, Osaka Metropolitan University
  • Kwangho Nam, The University of Texas at Arlington
  • Michael Feig, Michigan State University
  • Yasuhiro Matsunaga, Saitama University
  • Yong Min Rhee, KAIST

Lecturers for Afternoon Sessions


  • Wonpil Im (Lehigh University): CHARMM-GUI (general)
  • Nathan Kern (Lehigh University): Multicomponent Assembler
  • Turner Brown (Lehigh University): Membrane Builder
  • Sangjun Park (Lehigh University): Glycan
  • Donghyuk Suh (Lehigh University): Enhanced sampler, QM/MM, and constant-pH
  • Seonghoon Kim (MolCube, Inc): Free Energy Calculator


  • Chigusa Kobayashi (RIKEN R-CCS): GENESIS on Fugaku
  • Cheng Tan (RIKEN R-CCS): CG MD
  • Jaewoon Jung (RIKEN R-CCS): High-performance MD
  • Kiyoshi Yagi (RIKEN CPR): QM/MM
  • Shingo Ito (RIKEN CPR): QM/MM and enhanced sampling


Coming soon…
  • June 30th, July 1st, July 2nd: morning sessions for scientific lectures
  • June 30th, July 1st, July 2nd: afternoon sessions for hands-on tutorials


  • The workshop is accessible to all who register at https://forms.gle/kPSwWpYuttMSzpKr8 and is offered at no cost.
  • Should you encounter difficulties accessing the website, kindly email us your name, affiliation, and email address at iupab2024handson[at]ml.riken.jp (please substitute “[at]” with “@”).
Note: this website is designated for registering for the morning sessions (scientific lectures). If you wish to participate in the afternoon sessions (hands-on tutorials), please ensure to register through the official IUPAB2024 website.

Organizing Committee

  • Yuji Sugita, Chief Scientist at RIKEN CPR and Team Leader at RIKEN BDR, and R-CCS.
  • Wompil Im, Presidential Endowed Chair and Professor at Lehigh University.
  • Florence Tama, Team Leader at RIKEN R-CCS and Professor at Nagoya University.
  • Yasuhiro Matsunaga, Associate Professor at Saitama University.
  • Kei Moritsugu, Professor at Osaka Metropolitan University.