Moltemplate2.22.5 native conversion and template-roundtrip examples
Own12-bead harmonicchain:11bonds,K100,r0=1.3,m1,zero nonbonded,LAMMPS reducedLJ units.
Real500-step NVE,dt0.0001,11trajectoryframes,51thermorows;not fitted chemical polymer dynamics.
Native tools:moltemplate.sh,dump2data.py,raw2data.py,recenter_coords.py,extract_lammps_data.py,ltemplify.py,cleanup_moltemplate.sh.
DATA/RAW/XYZ,last and selectedframe,velocity-bearing DATA template,LT reconstruction,unused-type cleanup.
Controlled incomplete-tail input is rejected by installeddump2data;own keep-complete-frames.py retains only the byte-exact complete prefix through450,never fabricates a missingframe.
Data conversion is not a fullMD restart:fix/integratorstate is not preserved.
Recalculate fresh:sbatch job.slurm;withinallocatedresources:bash run.sh.
View realreference:bash show-reference.sh;re-analyze completedwork:bash analyze-results.sh.
Reference native outputs in reference-results/native;plots andCSV generated from realoutput.
LAMMPSCPU30Sep2026 with InteloneAPI2024.2/IntelMPI/MKL;Moltemplate existing Python3.11 environment;plotPython supplied by sisl0.16.4.
Not all32 installedMoltemplate publicentrypoints are covered here;other specialized converters remain separate tutorials.
