Development of interface for gromacs based MD simulation preparation

Molecular dynamics (MD) simulation is a critical method for understanding biological and chemical processes at the atomic level. However, this simulation, especially when performed using software such as GROMACS, requires both software knowledge and skills and hardware with high computational power. This creates an access barrier for many researchers and slows down scientific processes. In this study, we automated GROMACS-based simulation processes with a user-friendly web and cloud-based platform to facilitate simulation access and to produce a user-friendly interface. The system enables users to start the simulation by uploading protein and ligand files, visualise the results and share the results obtained. Thus, both users with limited software expertise were encouraged to enter this field and the productivity of experienced researchers was increased. The project was carried out by combining a web interface, local GROMACS servers and a cloud-based infrastructure. The files uploaded to the software web interface were transmitted to the GROMACS servers and the necessary additional files were downloaded over the internet and the standard GROMACS workflow was executed. Upon completion of the simulation, the system automatically generated graphical outputs such as RMSD, energy plots and atomic distance changes. These outputs were uploaded to a cloud server so that users can easily access the results on the web.