Moltemplate curve/polymer,MOL2 andPDB practical examples
Own13-site spline-guided harmonicchain,12backbonebonds;two crosslinks give14bonds.
K100,r01.3 andcrossK5,r02.6,mass1,zero nonbond;reducedLJ units,not a fitted chemical polymer.
Curve preprocessing uses version-pinned per-invocation solver adapter;see CURVE-ADAPTER-NOTE.txt.
Native genpoly_lt.py/genpoly_modify_lt.py generate LT from actual coordinates and zero-based modification locations3,8.
Own4-site MOL2 chain:3bonds,charges+0.1,-0.1,-0.1,+0.1;externalchargefile doublesvalues.
Zero pair style does not include Coulomb energy;charge import is a fileproperty example only.
Native mol22lt ignores MOL2 bond-order column;chemical forcefield typing remains user responsibility.
PDB synthetic5records demonstrate chain/residue/insertion/serialsorting andfixedcolumn extraction.
Installed pdbsort retains nonatom lines but moves them before atomrecords,includingEND;do not treat output as an in-place archival PDB rewrite.
Recalculate freshallocatedCPU resources:sbatch job.slurm;or bash run.sh withinallocation.
View true reference:bash show-reference.sh;re-analyze:bash analyze-results.sh.
Four genuine LAMMPSrun0 perqualifiedcontext;no MD or geometry relaxation claimed.
ExistingMoltemplate2.22.5/Python3.11 andLAMMPS30Sep2026/oneAPI2024.2/IntelMPI/MKL;plotPython via sisl0.16.4.
Sixadditional toolfeatures;remaining32-entrypoint census stays open.
