Molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes.
GENESIS (GENeralized-Ensemble SImulation System) is molecular dynamics for bimolecular systems such as proteins, nucleic acid, lipids, glycans, and their complexes. GENESIS is open source software distributed under the GPLv2 license.
Proteins and other macromolecules inside living organisms are responsible for many of the processes that are at the core of biological activity. Understanding the working mechanism of such molecules is one of the major challenges in biological research. In many cases, biological macromolecules use structural fluctuations or large-scale structural changes to perform their function. However, due to their extremely small size, capturing the movement of macromolecules in detail using experimental methods alone is difficult. In view of this, computer simulation methods have been widely adopted in recent years for calculating molecular motion.
GENESIS is software which applies the molecular dynamics (MD) method to capture molecular motion, it has the following features.
Algorithms for parallelization and acceleration are used to effectively utilize machines possessing a huge number of CPU cores, such as the K computer. High-speed calculations can also be performed on other architectures such as GPGPU machines, personal computers, and workstations. Due to these features, calculations of molecular systems of enormous size, which could not be performed in the past, have now become feasible.
Methods with high sampling efficiency, such as the replica-exchange MD method (Sugita & Okamoto, 1999) have been implemented. In these methods, multiple copies of the target system are generated and simulated simultaneously to facilitate the sampling of a large conformational space. Using these methods, it has become possible to investigate complex, large-scale conformational changes, which are difficult to observe using conventional MD calculations.
At present, we are continuing to develop new calculation methods and introduce them into GENESIS.
GENESIS is open source software distributed under the GPLv2 license.
Further information is available on the GENESIS website (English version), including available simulation methods, instructions on how to obtain the software, and topic-specific tutorials.