Introduction

This is the simplest possible htpolynet run: parameterize one small molecule (styrene), pack copies into a box, densify, and run a short anneal — no cure reactions, no capping, no iteration. It is a useful shakedown of a fresh install: if this build completes cleanly, the htpolynet ↔ AmberTools ↔ GROMACS plumbing is healthy and you can move on to the polymerizing examples.

It is also a reasonable way to produce an equilibrated liquid of a monomeric species — for example, as a precursor configuration for later cure runs, or as a starting point for small-molecule property estimates (density, free volume, etc.).

Set up a clean working directory and pull the example YAML:

$ mkdir my_liquid_styrene
$ cd my_liquid_styrene
$ htpolynet fetch-example 0
Fetched 0-liquid-styrene.yaml  (run with: htpolynet run 0-liquid-styrene.yaml)
$ ls
0-liquid-styrene.yaml

That single YAML is everything you need: it carries the styrene SMILES inline, so htpolynet materializes STY.mol2 for itself at the start of the run. No shell script, no pre-generated input files.