Molecular dynamics (MD) is a powerful tool used to study the evolution of molecular systems and predict their properties from the inherent interactions. GROMACS is a famous tool for MD and developed as open-source software. GROMACS is run from the command line with user-provided configuration files. However, the absence of a graphical user interface (GUI) of GROMACS and proper protocol to develop the input files (Ex: itp files, topology files, etc.) prevent the researcher from visualizing the MD trajectory in a real-time manner as well as addressing the structural problem. This issue was addressed by developing a graphical user interface of GROMACS as plugins for YASARA molecular graphics suite, called YAMACS. YAMACS is an open-source project and is available on GitHub (https://github.com/YAMACS-SML/YAMACS). The tool can perform MD simulations for protein, protein-ligand complex, membrane–protein complex, membrane-protein complex, and small molecule system. Easily YAMACS automatizes several steps of input file preparation and allows visualizing MD trajectory in real-time.
At this conference, I will present the application of YAMACS to simulate the complex sphingomyelin/POPC embedded in a membrane of POPC. I will also introduce a collaborative platform to create an open community of users and developers, extend the functionalities of YAMACS and improve the quality of computational drug design studies.
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