I will run molecular dynamics simulation and analysis

"Need reliable molecular dynamics MD simulation for your protein or protein-ligand complex? I provide research-grade MD simulation and analysis using GROMACS, helping researchers and students validate structural stability and binding behavior over time.

What I offer: MD simulations of proteins or protein-ligand complexes with system setup, energy minimization, equilibration, and production runs. Post-simulation analysis includes RMSD, RMSF, radius of gyration, hydrogen bond analysis, and optional MM-PBSA/GBSA binding free energy calculations.

Tools: GROMACS, VMD, PyMOL, Xmgrace for plotting.

You receive: A detailed PDF report with all analysis plots, raw trajectory/output files, and a clear summary of structural stability findings.

Why me: Hands-on experience across the full computational pipeline from docking to MD to free energy analysis so I understand how your simulation results fit into the bigger picture of your project.

Please have ready: Your protein structure (PDB file) and, if applicable, ligand structure (PDB/MOL2/SDF). Let me know your desired simulation length or leave it to my recommendation.

Message me your system details for a custom quote let's get your simulation