Tutorial 3 — Periodic box, temperature & pressure

Goal: move from an isolated chain to a periodic box, and learn the two ensembles COSMO supports out of the box: NVT (fixed volume) and NPT (fixed pressure, with a barostat that resizes the box). This is the foundation for any multi-chain / condensate run (Tutorials 5–6).

Time: a few seconds each on a CPU.

Files in this folder

File

Role

asyn.pdb

The Tutorial-1 chain again.

md_nvt.ini

NVT: temperature coupling on, pressure coupling off.

md_npt.ini

NPT: temperature and pressure coupling on.

run_simulation.py

Thin runner wrapper.

Background concepts

  • Periodic boundary conditions (pbc = yes). The chain sits in a box that tiles space; a bead leaving one face re-enters the opposite face. Set the size with box_dimension — a scalar L for a cubic box, or [x, y, z] for a rectangular one (nanometers). PBC is required for pressure coupling and for any multi-chain density study.

  • NVT (canonical). tcoupl = yes, pcoupl = no. The Langevin thermostat holds temperature at ref_t; the box volume is fixed. This is the default ensemble for sampling at a chosen concentration.

  • NPT (isobaric). tcoupl = yes, pcoupl = yes. COSMO adds a Monte Carlo barostat automatically (you do not write any extra code) that rescales the box to hold the pressure at ref_p, attempting a move every frequency_p steps. Use it to relax a system to a sensible density before a production run. pcoupl = yes requires pbc = yes — the runner asserts this.

Step-by-step

1. Run NVT

python run_simulation.py -f md_nvt.ini

Outputs go to traj/asyn_nvt.*. The box stays 30 nm on a side the whole run.

2. Run NPT

python run_simulation.py -f md_npt.ini

Outputs go to traj/asyn_npt.*. In the build log you’ll see the barostat being added (it is not present in the NVT run). Over the run the box dimensions drift as the barostat equilibrates the volume toward ref_p = 1 bar.

3. Compare

Both runs write the standard *.log (see Tutorial 1 for the columns). The NPT log reflects a system whose volume is being adjusted; the NVT log is at fixed volume. For a single dilute chain the energetic difference is small — the point here is the mechanism: NPT is how you find a reasonable box/density, after which you typically switch to NVT for production (exactly the slab recipe in Tutorial 5).

Try next

  • Shrink the box (box_dimension = 15) and watch how PBC + a small box start to matter as the chain “sees” its periodic image.

  • Use a rectangular box, e.g. box_dimension = [30, 30, 60], the elongated geometry used for slab/LLPS simulations (Tutorial 5).

  • Move to Tutorial 4 to restart a run from its checkpoint and tour every output file in detail.