GENESIS – All-atom Molecular Dynamics Simulation

In 1992 I attended a molecular graphics visualization and simulation somewhere in Texas, organized by Keck. One of the presenter had a movie of molecular dynamics of a protein that forever changed my mental view of  the 3D structure of a protein: the atoms “wiggled” and it made clear with a stunning visual depiction that the molecules were not “frozen” like statues as they appeared in ordinary molecular graphics programs of the time (e.g. UCSF MIDAS-Plus, BioSym InsightII, etc.) but were more like rubber jelly, which made more sense. It was a “eureka” moment for me. Nowadays it is pretty common to find youtube videos with such simulations. Today I found this one that show how things have evolved since 1992:

In the caption they specify that the simulation was done with a software called GENESIS which recently released version 1.4 in October 2019. GENESIS is an acronym for “GENeralized-Ensemble SImulation System.” GENESIS is open-source

On the web page they specify: Molecular dynamic (MD) trajectories obtained by GENESIS can be visualized with VMD and other software. However, it is unsure that the beautiful video was rendered with VMD.

Note: VMD is from the University of Champaign-Illinois, that was developed to render the MD from their own simulation software NAMD.

Fun note: On their slide presentation All‐atom molecular dynamics simulations of biological systems using supercomputers (PDF slides – archived version today) they show that the computation was done on the K computer (4th faster computer) so we can’t compete with a Mac or PC! One slide shows picture of the development team.