molecular-dynamics

You can run molecular dynamics simulations and analyze trajectories by integrating OpenMM for system preparation, energy minimization, and NVT/NPT production runs, followed by MDAnalysis to compute RMSD, RMSF, and contact maps.

The best way to prepare a protein system for MD simulations is to apply force fields and solvation, then perform energy minimization using OpenMM to remove steric clashes and ensure structural stability before equilibration.

Yes, the molecular dynamics workflow supports ligand binding analysis by utilizing MDAnalysis to evaluate trajectory data, calculate contact maps, and generate free energy surfaces for biophysics and drug discovery studies.

Yes, you can use OpenMM and MDAnalysis to study protein stability after a mutation by running production simulations and analyzing the resulting trajectories for RMSD and RMSF fluctuations.

You need OpenMM, MDAnalysis, and additional Python tools like NumPy, SciPy, Matplotlib, Pandas, and NGLView installed to handle system preparation, simulation execution, trajectory analysis, and molecular visualization.

You can analyze MD simulation trajectories to calculate RMSD and RMSF by loading the production run output into MDAnalysis, which processes the trajectory frames to measure structural deviations and fluctuations over time.