IUPAB2024 Hands-on Training Program
CHARMM-GUI/GENESIS MD Tutorial
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.
- Please note: We do not provide lunch box for hands-on students and participants (except for invited speakers, lecturers, and TAs). Additionally, there are few restaurants and convenience stores nearby. We recommend bringing your own food in the morning.
Workshop Overview
Objective: Our workshop serves two main purposes:
- To facilitate discussions on the recent advancements in computational biophysics research.
- To provide on-site, hands-on tutorials on CHARMM-GUI and GENESIS, enabling participants to apply these tools effectively in their research endeavors.
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.
Program
Day 1: 30 June 2024 (Sun)
|
| 8:40 – 9:00 |
Registration |
| 9:00 – 9:10 |
Welcome address by Wonpil Im (Lehigh University) |
| Session 1 |
Molecular Dynamics Theories and Methods (chair: Yasuhiro Matsunaga) |
| 9:10 – 9:40 |
Helmut Grubmüller (Max Planck Institute for Multidisciplinary Sciences) |
|
Constant pH Simulations with FMM and solvation shell entropies |
| 9:40 – 10:10 |
Kei Moritsugu (Osaka Metropolitan University) |
|
Weighted Ensemble for Biomolecules |
| 10:10 – 10:40 |
Ana Damjanovic , Juyong Lee, Bernard Brooks (NIH) |
|
Constant pH Replica-Exchange Methods
|
| 10:40 – 11:00 |
COFFEE BREAK |
| Session 2 |
Enzyme Mechanisms (chair: Kiyoshi Yagi) |
| 11:00 – 11:30 |
Kwangho Nam (The University of Texas at Arlington) |
|
Advancements in multiscale QM/MM and free simulation methods for enzyme modeling |
| 11:30 – 12:00 |
Youngmin Rhee (KAIST) |
|
Following photodynamics in biology: non-adiabatic dynamics simulations with conventional MD packages |
| 12:00 – 13:30 |
LUNCH
|
| 13:30 – 18:00 |
Scientific Discussion (6F, 8F) |
| GENESIS |
Hands-on Part 1 |
|
Lecturer: Chigusa Kobayashi (RIKEN)
|
| 13:30 – 14:30 |
GENESIS basics and GENESIS on Fugaku |
| 14:30 – 15:00 |
Hands-on GENESIS |
| 15:00 – 15:20 |
BREAK |
| CHARMM-GUI |
Hands-on Part 1 |
|
Lecturer: Wonpil Im (Lehigh University) |
| 15:20 – 16:20 |
Introduction of CHARMM-GUI and Membrane Builder |
| 16:20 – 17:20 |
Hands-on CHARMM-GUI |
| 17:20 – 18:00 |
BREAK |
Day 2: 01 July 2024 (Mon)
|
| Session 3 |
Membrane Biology (chair: Florence Tama) |
| 9:00 – 9:30 |
Chen Song (Peking University) |
|
Gating mechanism of the mechanosensitive ion channel NOMPC: new insights from molecular dynamics simulations |
| 9:30 – 10:00 |
Jana Shen (University of Maryland) |
|
Drug-membrane partitioning and crossing from unbiased molecular dynamics coupled with proton titration |
| 10:00 – 10:30 |
Ben Corry (Australian National University) |
|
Molecular simulation of membrane channels, transporters, and receptors |
| 10:30 – 10:50 |
COFFEE BREAK |
| Session 4 |
Modeling of Cellular Components, Part I (chair: Yasuhiro Matsunaga) |
| 10:50 – 11:20 |
Jianhan Chen (University of Massachusetts) |
|
Coarse-grained simulations of protein and RNA phase separation |
| 11:20 – 11:50 |
Michael Feig (Michigan State University) |
|
Multi-scale modeling of biomolecular condensates |
| 11:50 – 13:15 |
LUNCH |
| 13:15 – 18:00 |
Scientific Discussion (6F, 8F) |
| Fugaku Tour |
Instructor: Chigusa Kobayashi |
| 13:15 – 14:20 |
GROUP 1 |
| 13:55 – 14:55 |
GROUP 2 |
| GENESIS |
Hands-on Part 2 |
| 14:30 – 15:30 |
Lecturer: Cheng Tan (RIKEN) |
|
Coarse-grained simulations in GENESIS (Lecture + Hands-on) |
| 15:30 – 16:30 |
Lecturer: Jaewoon Jung (RIKEN) |
|
High-performance computation with GENESIS (Lecture + Hands-on) |
| 16:30 – 16:45 |
BREAK |
| CHARMM-GUI |
Hands-on Part 2 |
|
Lecturer: Nathan Kern (Lehigh University) |
| 16:45 – 17:15 |
Multi-component assembler |
| 17:15 – 18:00 |
Hands-on multi-component assembler |
Day 3: 02 July 2024 (Tue)
|
| Session 5 |
Modeling of Cellular Components, Part II (chair: Kei Moritsugu) |
| 9:00 – 9:30 |
Gerhard Hummer (Max Planck Institute of Biophysics) |
|
Integrating molecular dynamics simulations and experiments |
| 9:30 – 10:00 |
Naoto Hori (University of Nottingham) |
|
Coarse-grained simulations of RNA folding and misfolding |
| 10:00 – 10:20 |
COFFEE BREAK |
|
|
| 10:20 – 10:50 |
Alberto Perez (University of Florida) |
|
Synergizing simulations and experiments: faster exploration of biologically relevant states |
| 10:50 – 11:20 |
Florence Tama (RIKEN) |
|
Unraveling the Structure and Dynamics of Biomolecules via Integrative Modeling |
| 11:20 – 11:50 |
Yasuhiro Matsunaga (Saitama University) |
|
Integrative Modeling of Protein Dynamics from High-speed Atomic Force Microscopy and Molecular Dynamics Simulations |
| 11:50 – 12:00 |
Closing Remarks to the morning sessions by Yuji Sugita (RIKEN) |
| 12:00 – 13:30 |
LUNCH |
| 13:30 – 17:10 |
Scientific Discussion (6F, 8F) |
| GENESIS |
Hands-on Part 3 |
|
Lecturer: Shingo Ito (RIKEN) |
| 13:30 – 15:00 |
Generalized-ensemble simulations using GENESIS |
| 15:00 – 15:30 |
BREAK |
| CHARMM-GUI |
Hands-on Part 3 |
|
Lecturer: Donghyuk Suh (Lehigh University) |
| 15:30 – 16:00 |
Enhanced sampler |
| 16:00 – 17:00 |
Hands-on enhanced sampler |
| 17:00 – 17:10 |
Yuko Okamoto (Nagoya University) |
|
Closing Remarks |
Teaching Assistants
- GENESIS: Shingo Ito, Jaewoon Jung, Chigusa Kobayashi, Cheng Tan, Diego Ugarte La Torre, Kiyoshi Yagi, Yangyang Zhang, Azuki Mizutani, Masahiro Motohashi (RIKEN), Song-Ho Chong (Kumamoto University/RIKEN)
- CHARMM-GUI: Turner Brown (Lehigh University), Seonghoon Kim (MolCube Inc.)
Registration
Organizing Committee
- Yuji Sugita, Chief Scientist at RIKEN CPR and Team Leader at RIKEN BDR, and R-CCS.
- Wonpil 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.
Sponsors
Supported by the COE research grant in computational science from Hyogo Prefecture and Kobe City through Foundation for Computational Science; MEXT “Program for Promoting Researches on the Supercomputer Fugaku” (Development and application of large-scale simulation-based inferences for biomolecules JPMXP1020230119); RIKEN Cluster for Pioneering Research; RIKEN Center for Biosystems Dynamics Research; Biomolecular Simulation and Modeling subgroup in the biophysical society of Japan.