Molecular Dynamics Simulations of Protein Structure using Gromacs

Molecular dynamics (MD) simulations are computational methods that monitor the temporal evolution of interacting atoms and molecules through the numerical integration of Newton’s laws of motion. This enables researchers to examine the dynamics and behaviour of molecular systems, which are essential for comprehending biomolecular interactions and have significant implications in fields such as drug discovery, protein engineering, and structural biology. To address the increasing interest in learning MD simulations on Linux using GROMACS, a flexible, open-source software tool utilized for conducting molecular dynamics (MD) simulations, especially for biomolecular systems like proteins, lipids, and nucleic acids, which help researchers simulate the movement of atoms and molecules over time based on classical mechanics. The upcoming workshop on Molecular Modelling and Dynamics Simulations of Biomolecule Structure will provide participants with a distinctive learning opportunity, featuring recorded videos for future reference. Attendees will acquire both theoretical and practical skills in modelling biological molecules, solvating proteins, conducting minimization, equilibration, and simulations, as well as analysing the outcomes. Offering a thorough introduction to molecular simulation using GROMACS, the workshop blends theoretical knowledge with practical applications, presenting an invaluable chance for researchers and professionals to incorporate MD simulations into their work.

To facilitate the MD simulation of biomolecule to explore biological phenomena and the behaviour at the molecular level.

• To analyse the dynamic characteristics of molecular systems such as proteins, lipids, and nucleic acids at an atomic scale, enabling researchers to gain insights into their structure, interactions, and behaviour, which ultimately assists in unravelling biological processes and developing novel therapeutics.
• To represent and examine the arrangement of molecules and how they evolve over time, which is essential for comprehending their function.

This workshop intends to provide an arena for students, faculty and researchers in discussing the following topics as well as to provide hands on training in the following key areas for the new drug development.

• Undergraduate/Postgraduate degree in Bioinformatics, Biotechnology, Biophysics, Computational Biology, or related fields.
• Researchers and professionals in pharmaceutical sciences, structural biology, or computational chemistry.
• Individuals with a keen interest in molecular modeling, drug discovery, and protein-ligand interactions.

• Understanding of molecular dynamics and protein structure simulations.
• Proficiency in using GROMACS for biomolecular simulations.
• Ability to analyze and interpret protein-ligand interactions.
• Skills in preparing simulation input files and running MD simulations.
• Hands-on experience with visualization and trajectory analysis tools.