Equilibrate

Step by step

1. Pick a protocol

   Larsen et al. 21-step (2011) (the default) compresses and decompresses between T max / P max and your targets; Simulated annealing cycles between T low and T high; MD push-off separates overlaps; Custom (edit the text) lets you write the stages yourself.

2. Set the targets

   T final 300 K, T max 600 K, P final 1 atm. Time × stretches or shortens every stage. The stages are listed, editable, under Stages (editable text).

3. Ask for convergence

   Switch on Production blocks until converged: CAPS adds 20 ps blocks (up to 20) until density, energy and Rg stop drifting.

   Optionally require the mean-square internal distances to converge too, to RIS polyethylene or a curve from a file.

4. Long chains: regrow the ends

   Chain ends · configurational-bias Monte Carlo → Regrow chain ends relaxes chain conformations faster than MD alone.

5. Press Equilibrate

   Watch the plots and the Criteria panel. Accept now keeps the current state; Save trajectory… writes the frames.

The same without the Studio

Every Studio page calls the same core as the caps command and the caps Python package, so a step you clicked can be repeated in a script.

caps equilibrate cell_min.data -o cell_eq.data --protocol larsen21 \
    --tfinal 300 --pfinal 1 --until-converged --log thermo.csv

import caps

d = caps.open("cell_min.data")
ok = d.equilibrate("larsen21", temperature=300, pressure=1, until_converged=True)
d.save("cell_eq.data")

Where to go next

RunDynamicsNVE, NVT, NPT or NPH molecular dynamics in CAPS, with live snapshots, or a LAMMPS / GROMACS deck.Analyse & exportAnalyzeDensity, g(r), chain statistics, Tg, moduli, diffusion, free volume, interfaces and crosslink density — each with CSV.

Read more