Workshop on molecular dynamics based binding free energy calculations,
post-processing of trajectories and force field development
Nov.20 (Wed.) – 22 (Fri.), 2019
Centre of New Technologies, University of Warsaw, Warsaw, Poland

General Information

Molecular dynamics (MD) simulation is an indispensable tool for biological science, which provides molecular-level details of dynamical processes of complex biomolecular systems. This workshop is intended for those interested in running and analyzing the MD simulations of biomolecules. The participants will learn how to model, simulate, and analyze complex biomolecular systems using GENESIS (GENeralized-Ensemble SImulation System), MINT (Motif Identifier for Nucleic acids Trajectory), and RedMDStream.


The workshop will be held November 20-22, 2019 at the Lecture Hall 0187 (ground floor) of the Centre of New Technologies, University of Warsaw, Banacha 2C. Please refer to the following web sites for more information on the location. Centre of New Technologies

Scientific Program

November 20 (Wednesday)

<< Coffee available >>
12:30 – 13:00 Pre-opening Session
Help with software installation
13:00 – 13:30 Yuji Sugita (RIKEN Cluster for Pioneering Research)
Overview of GENESIS
13:30 – 14:30 Jaewoon Jung (RIKEN Center for Computational Science)
General introduction of MD & Performance optimization of GENESIS
<< Coffee Break >>
15:00 – 16:30 Chigusa Kobayashi (RIKEN Center for Computational Science)
Quick start of GENESIS – Demonstration and hands-on tutorial (*)
16:30 – 17:20 Suyong Re (RIKEN Center for Biosystems Dynamics Research)
An application of GENESIS: Simulating protein-ligand bindings

November 21 (Thursday)

<< Coffee available >>
9:30 – 11:00 Takaharu Mori (RIKEN Cluster for Pioneering Research)
Modeling complex biological systems – Demonstration and hands-on tutorial (*)
11:00 – 11:50 Maciej Jasiński (University of Warsaw)
Analysing MD trajectories with MINT
<< Lunch and coffee >>
13:00 – 13:30 Joanna Trylska (University of Warsaw)
Coarse-grained models and force fields of biomolecules
13:30 – 15:00 Joanna Trylska and Natalia Ostrowska (University of Warsaw)
Optimization of force field parameters (RedMDStream)

November 22 (Friday)

09:30 – 12:00 Q&A and Free discussion
Topics: practical usages of GENESIS, MINT, and RedMDStream
12:00 – 13:00 CeNT seminar: Dr. Yuji Sugita (RIKEN Cluster for Pioneering Research)
Lecture Hall 1130 (1st floor) Click here for details


The registration was closed because all slots were filled. Thank you for your interest.

(*) Regarding the hands-on tutorial, participants are encourage to compile the latest version of GENESIS (version 1.4) which is now available on the GENESIS Web site. Users may refer to the manual (Chapters 2 ( Getting Started) and 22 (Appendix)) for the compilation. Please send e-mail to Dr. Suyong Re (suyongre[at] if you find any trouble compiling GENESIS. We are planning to send the files used for demonstrations/hand-on tutorials to the participants before the workshop. The participants without the pre-compiled GENESIS are still welcome to learn how GENESIS works through our demonstration.

Organizing Committee

Yuji Sugita Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research
Joanna Trylska Biomolecular Machines Laboratory, Centre of New Technologies, University of Warsaw
Suyong Re Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research
Marta Kulik Electron Density Modelling Group, Biological and Chemical Research Centre, University of Warsaw


For any questions regarding the workshop, please send an email to Dr. Suyong Re (suyongre[at] or Dr. Marta Kulik (m.kulik[at]