HOLE2.3.1 ApacheLicense / GNUFortran13.3.0 and mdahole2 0.5.0 / MDAnalysis2.9.0.
Build is private totools/hole2; no compiler/library/sharedmodule changes. First setup downloads pinned2.5MB Apache source and compiles sequentially (upstream Makefile updates shared archive, so use-j1). No native vendor binary is bundled.
bash setup.sh
bash run.sh
bash verify.sh
bash plot.sh
Actual gramicidin single272atom structure and upstream elNemo mode7 eleven264atom normalmode models, select0,2,4,6,8,10. Normalmode perturbations are not MD or physical time.
Channel axis is y. sample0.2A yields sampled planes plus native Cartesian-midpoint clearance points; profile spacing may be0.1A. Auxiliary SPH residue-888 surfaceclosure spheres are separated from physical pore points. All sampled+midpoint clearance values independently checked.
No conductance, permeability, freeenergy or biological gating kinetics is claimed. Input structures and librarywheel retain upstream provenance/licenses.
