Results

At the end of the run, proj-N/systems/final-results/ contains:

• final.gro, final.top, final.tpx, final.grx — the densified, post-anneal liquid in GROMACS-friendly form.

• final.viz.psf, final.viz.tcl — VMD-friendly companion files. The PSF carries the real bond topology and the TCL helper trims bonds that wrap across the periodic image, so VMD does not draw the spurious long bonds you would otherwise see in a periodic box. Open with:

  $ vmd final.viz.psf final.gro -e final.viz.tcl
  

A useful sanity check: read off the final box volume and the total mass (1000 × styrene = 1000 × 104.15 g/mol) to compute density, and compare to liquid styrene’s literature value of ~909 kg/m³ at 25 °C. Because the equilibration is deliberately short, expect the result to approach but not match the literature value — the point of this example is plumbing, not production-quality property estimation.

Post-build analyses

The comment block at the top of 0-liquid-styrene.yaml sketches an htpolynet analyze configuration that runs three quick analyses on the densification output: a trajectory check, a methods report, and a freevolume calculation. Save those YAML lines into ck.yaml and run:

$ htpolynet analyze -cfg ck.yaml -ocfg 0-liquid-styrene.yaml -proj proj-0

Results land under proj-0/analyze/{check,report-methods,freevolume}/. The Post-build simulations and analyses section below shows the recommended postsim and analyze workflow for this system; DGEBA-PACM Epoxy Thermoset walks through the full set of techniques (annealing, ladders, deformation, free volume) with real production-quality plots for comparison.