Post-build simulations and analyses

Liquid styrene is not polymerized, so post-build “production” measurements like glass-transition temperature or Young’s modulus are not meaningful here. What we can do — and what is useful as a sanity check — is to equilibrate the as-built liquid further at 300 K and then measure its density and fractional free volume.

The DGEBA-PACM Epoxy Thermoset walks through the full set of postsim and analyze techniques in detail; this section just shows the minimum useful run for an unpolymerized liquid.

The postsim configuration

Create postsim.yaml in the project base directory:

- equilibrate:
    input_top: systems/final-results/final.top
    input_gro: systems/final-results/final.gro
    T: 300
    ps: 100

Run it:

$ htpolynet postsim -cfg postsim.yaml -ocfg 0-liquid-styrene.yaml -proj proj-0

This produces proj-0/postsim/equilibrate/ with the usual Gromacs outputs plus an on-the-fly density-vs-time plot.

Density during equilibration

Placeholder

TODO: insert the rho_v_ns.png plot from proj-0/postsim/equilibrate/ and report the mean equilibrated density (kg/m³ or g/cc) here. Note whether the system has reached a stable density (i.e., the trace is flat over the second half of the trajectory).

Free volume

Use htpolynet analyze with a one-line config to invoke gmx freevolume on the equilibration trajectory. Create fv.yaml:

- command: freevolume

Then:

$ htpolynet analyze -cfg fv.yaml -proj proj-0

The output lands in proj-0/analyze/freevolume/.

Placeholder

TODO: report the fractional free volume (and standard error) from proj-0/analyze/freevolume/ffv.dat here. For unpolymerized small-molecule liquids the FFV is typically in the 0.20–0.30 range; values much outside that suggest the equilibration was too short.