YAMACS: A Python Based Tool Kit for GROMACS

• Published in: Medical Sciences Forum
• Main Authors: Arkadeep Sarkar, Lucia Sessa, Luigi Di Biasi, Stefano Piotto
• Format: Article
• Language: English
• Published: MDPI AG 2022-11-01
• Subjects: molecular dynamics; GROMACS; YAMACS; YASARA
• Online Access: https://www.mdpi.com/2673-9992/14/1/98

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 the YASARA molecular graphics suite, called YAMACS. YAMACS is an open-source project and is available on GitHub. The tool can perform MD simulations for protein, protein–ligand complexes, membrane–protein complexes, membrane–protein complexes, and small molecule systems. Easily YAMACS automatizes several steps of input file preparation and allows visualizing the 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.