mdanalysis-trajectory-analysis

name	mdanalysis-trajectory-analysis
description	Analyze OpenMM, GROMACS, and other molecular dynamics trajectories with MDAnalysis using topology-aware selections, periodic-boundary handling, prespecified observables, convergence checks, and uncertainty estimates.
license	MIT

MDAnalysis Trajectory Analysis

Workflow

1. Follow $cx-compute-environment; ask once before installing a pinned MDAnalysis stack or processing a large trajectory.
2. Verify topology/trajectory compatibility, atom ordering, units, frame times, periodic box, stage boundaries, and missing/corrupt frames. Preserve raw files.
3. Prespecify selections, alignment reference, PBC transformations, equilibration discard, stride, observables, and success criteria before viewing comparisons.
4. Compute only scientifically relevant observables: RMSD/RMSF, distances, contacts, hydrogen bonds, secondary structure, radius of gyration, SASA, clustering, or dimensionality reduction. Save scripts/configs and derived data.
5. Estimate autocorrelation/effective samples; use block bootstrap or independent replicas for uncertainty. Plot time series as well as aggregate distributions.
6. Record versions, commands, selections, transformations, and checksums under artifacts/<run-id>/analysis/ and review with $science-review.

Boundaries

• Alignment can hide domain motion; state the fitted atoms and show alternatives when conclusions depend on them.
• Frames are autocorrelated, not independent replicates.
• RMSD plateau alone does not establish equilibrium, convergence, or binding.