MDAnalysis2.9 eight native tools on real completed GROMACS NPT water/ubiquitin and LAMMPS reduced-unit bead-spring trajectories. Run bash run.sh in new directory; existing qvasp2.26 Python environment is used only for MDAnalysis, no qvasp/VASP call. All results/plots are postprocessing, no newMD. NativeSETTLE SOL topology supplies explicit charges/masses/connectivity, not guessedPDBbonds. NPT cell varies: fixedcellLinearDensity excluded. Native dielectric finite51frames is not statistical convergence. Nativepolymerfit uses rewoundframe0bondscale and has24pctfitresidual: not materialpersistence. Polymerlengthsigma/time tau, notAngstrom. ProteinDistanceMatrix uses commonreferencealignedCA, no extra pairwisefit; no diffusionmap/freeenergyclaim. Every numeric field is included.
LAMMPSDUMP dt is the integration step0.002 in tau; native saved-step numbers0,200,...20000 give frame times0,0.4,...40tau. MDAnalysis default time labels are not physical ps for this reduced-unit trajectory.
