Results

After the build completes, the project directory proj-0/ contains the final Gromacs topology (*.top) and coordinate (*.gro) files for the cured polystyrene system, along with a full archive of intermediate files.

Using htpolynet plots

htpolynet ships with a plotting subcommand that reads diagnostics.log and generates summary figures:

$ htpolynet plots -diag diagnostics.log

This produces plots of conversion vs. time, density evolution, and per-iteration bond counts, which give a quick picture of how the cure progressed.

As a further exercise, copy pSTY.yaml to pSTY-low.yaml, change desired_conversion from 0.95 to 0.50, and run a second build:

$ cp pSTY.yaml pSTY-low.yaml
$ # edit pSTY-low.yaml: desired_conversion: 0.50
$ htpolynet run -diag diagnostics-low.log pSTY-low.yaml &> console-low.log &

The second build will populate proj-1/. Comparing plots from diagnostics.log and diagnostics-low.log shows how cure conversion affects system density and chain structure.

Post-simulation analyses

Once you have a cured polystyrene system, you can use htpolynet postsim and htpolynet analyze to run production MD and compute properties such as the glass-transition temperature. These workflows are described in the post-simulation analyses tutorial.