GENeralized-Ensemble Simulation System(GENESIS) is molecular dynamics and modeling software for proteins or other biomolecular systems. It consists of two simulators, SPDYN and ATDYN. SPDYN shows high performance on massively parallel supercomputers like K computer in RIKEN AICS. ATDYN allows you to perform multi-scale simulations using coarse-grained models and all-atom models. Replica-exchange molecular dynamics methods or other generalized-ensemble algorithms are currently available only in ATDYN.

The software has been developed mainly by the people who are working in Computational Biophysics Research Team in RIKEN AICS. Several people in RIKEN QBiC and RIKEN Theoretical Molecular Science Laboratory also have participated in the development.

Obtaining GENESIS

GENESIS is released under GPLv2 license. However, for statistical survey of downloads, we ask a favor of you to fill in the registration form and send it to us via e-mail (genesis"at"riken.jp (change "at" to @)). After completion of your registration, you will receive an E-mail from us, which indicates the link of GENESIS source code.

Registration form: MS Word, PDF

Document

A user guide is provided for instruction of installation, usage, and some tutorials. This user guide will be updated without notification.

GENESIS User Guide (PDF, 2.6MB)

How to cite GENESIS in publication

Any published work which uses GENESIS might include the reference below:

Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig, and Yuji Sugita.

"GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.", WIREs Computational Molecular Science (DOI: 10.1002/wcms.1220)

Other GENESIS-related papers

News


May 8, 2015
GENESIS 1.0 is released.
GENESIS 1.0 has been installed on K computer.

May 30, 2014
GENESIS is upgrated (pre-release 0.2).
GENESIS 0.2 has been installed on K computer.

May 30, 2014
Training of GENESIS will be held on Jun. 17th, 2014 (Kobe, AICS).
Further information: Announce of training (AICS, Japanese)

March 31, 2014
GENESIS 0.1 is pre-released.
GENESIS 0.1 has been installed on K computer. Detailed information is available on K portal.

Note

In computational neural science, there is another "GENESIS (General Neuron Simulation System)" simulator, which has much longer history in the development [The Book of GENESIS]. Our "GENESIS" has been developed independently to investigate conformational dynamics of proteins, nucleic acids, biological membranes, and other biomolecules.