Molecular Dynamics of Proteins Research Project
Research mentor:
4.0
Run a complete protein simulation in GROMACS starting from no Linux experience. You build the system, run the dynamics yourself, and finish with an analysed trajectory and the RMSD, RMSF and radius-of-gyration plots that describe it.
Explore free modules at no cost to see if this research project matches your learning goals.
Project Objectives
1. Build Your Simulation Environment
Set up a complete molecular dynamics environment from scratch by installing and configuring Linux, the terminal, and GROMACS, even with no prior computational experience.
2. Prepare the Protein System
Prepare a real protein for simulation, from downloading and cleaning the PDB structure to generating its topology and building a solvated, ionized system.
3. Run the Full Simulation Workflow
Run and verify the full simulation workflow, including energy minimization, NVT and NPT equilibration, and production MD, and correctly interpret the outputs at each stage.
4. Troubleshoot and Complete a Project
Independently manage, troubleshoot, and complete a publication quality apo protein simulation, then document and present the results like a researcher.