scientific-md-simulation

To compute RMSD and RMSF time-series from a molecular dynamics trajectory, apply an analysis pipeline to standard formats like DCD/XTC/TRR and PSF/PDB. The process calculates per-frame structural deviations and flexibility, outputting consolidated time-series metrics for stability assessment.

Hydrogen bonds and Solvent Accessible Surface Area (SASA) are key metrics used to evaluate protein-ligand interactions and solvent exposure in MD simulations. Analyzing these alongside radius of gyration provides per-frame time-series data to rigorously assess complex stability.

Yes, you can analyze DCD and XTC trajectory files using a PSF topology. The analysis supports standard trajectory and topology formats including TRR and PDB, enabling comprehensive structural evaluations like radius of gyration and SASA for protein-ligand systems.

To generate ligand force-field parameters for an MD workflow, apply OpenFF parameterization to the ligand structure. This process supports end-to-end MD workflows by producing the necessary force-field parameters for rigorous simulation and analysis.

The best way to extract per-frame metrics from a 100 ns protein-ligand trajectory is running a comprehensive MD analysis pipeline. It computes RMSD, RMSF, Rg, hydrogen bonds, and SASA, producing publication-ready per-frame time-series and a consolidated summary.