Gmx_qk: An Automated Protein/Protein–Ligand Complex Simulation Workflow Bridged to MM/PBSA, Based on Gromacs and Zenity-Dependent GUI for Beginners in MD Simulation Study
Harvinder Singh, Anupam Raja, Ajay Prakash, Bikash Medhi
Abstract
Open-source MD simulation tools provide academics and low-income countries with the ability to compete in drug discovery advancements. Gromacs is a well-known and established MD simulation tool, among others. Although command-line tools offer full flexibility to users, they require expertise and familiarity with the UNIX operating system. In this context, we have developed an automated bash workflow that enables users with minimal knowledge of UNIX or command-line tools to run protein/protein-ligand complex simulations bridged to MM/PBSA calculations. The workflow provides information to the user using Zenity widgets and requires minimal intervention, such as energy minimization, simulation duration, and output file naming. It initiates MD simulations within a few seconds (energy minimization, NVT, NPT, and MD) after taking input files and parameters, which takes 20-30 min in a command-line-based protocol. The single workflow also helps users to produce reproducible research results with fewer errors. The workflow is available at the GitHub repository: https://github.com/harry-maan/gmx_qk.