MDAnalysis2.9.0 real ubiquitin protein analysis:76residues1231atoms1237bonds,51 actualframes0..100ps selectedstride20from1001completedGROMACSframes. No newMD and no equilibrium/foldingkinetics claim.
Run bash run.sh using the installedqvasp2.26 Python environment; qvasp/VASP are not called. Other machines set ANALYSIS_PYTHON to a Python with compatibleMDAnalysis2.9/NumPy/SciPy/Matplotlib. New results/plots directories required.
Eight native modules: DSSP,BAT,Ramachandran,Janin,Contacts,GNM,PCA,HELANAL. Original XTC/TPR are ownedcompletedMD data. CurrentGROMACS2026 TPR138 is not directlyreadable byMDA2.9. protein-conect.pdb and topology-metadata.json derive from nativeGROMACSeditconf-conect/dump; masses/charges/elements are NOT guessed. export-topology.sh repeats onlythattoolconversion, notMD.
DSSP recognizes actualterminalOC1 plusinternalO. This maps helix/sheet/loop to3classes, not separatealpha/pi/310subclasses. HELANAL recommendednumbers use nativehelix_analysis onfloat64-promotedinput; originalclass32 strictrotationerror0.000384927deg is retained in precision-limits.json, original1e-5degreecriterion notrelaxed. Promoting arithmetic does not improve original XTC coordinateprecision. BAT fullCartesianroundtrip preserves3Ncoordinates. GNM eigenvectors andPCA components have sign/degeneracy freedom; compare eigenvalues/covariances/projectors, not arbitrarynullspacevectors.
Reference arrays contain all fields. precision-limits.json explains arithmetic precision; original trajectory information is unchanged.
