Run with implicit solvent#

You will learn: how to run a simulation where the solvent is modelled as a continuum dielectric (GBSA-OBC) rather than explicit water molecules.

Prerequisites:

  • ACEMD installed.

  • An AMBER topology (.prmtop) built for implicit solvent — no water box, no ions, and the right Generalised Born radii baked into the PRMTOP. A topology built for explicit solvent won’t give correct dynamics here, even if you turn implicitsolvent: true on at runtime. With HTMD, build() accepts an igb/implicit-solvent flag that produces the right PRMTOP; see HTMD’s docs.

  • A coordinate file for the solute (PDB or any moleculekit-readable format).

Implicit solvent is much cheaper per step than explicit-water simulations and is useful for small-molecule conformational sampling, peptide-folding studies, and quick equilibrations. The trade-off: no water-specific dynamics (hydrogen-bond reorganisation, water-mediated interactions) and inflated diffusion coefficients.

Setup#

input.yaml#
structure: solute.prmtop
coordinates: solute.pdb
implicitsolvent: true
igb: 2
thermostat: true
run: 100ns

What’s different from an explicit-water run:

  • implicitsolvent: true — turns on Generalised Born implicit solvent.

  • igb: 2 — the implicit-solvent model. 2 is OBC1, the recommended default. Valid values: 1 (HCT), 2 (OBC1), 5 (OBC2), 7 (GBn), 8 (GBn2). See the OpenMM AMBER implicit-solvent table.

  • No boxsize — non-periodic system.

  • No barostat — no box volume to regulate.

  • No cutoff — ACEMD uses a 20 Å non-periodic cutoff internally for implicit solvent. The top-level cutoff option is ignored on this path.

Run#

acemd

Gotchas#

  • AMBER only. ACEMD’s implicit-solvent path is built around AMBER’s Generalised Born radii. The flag isn’t gated on topology type, so a CHARMM PSF or OpenMM-XML setup will run but produce wrong physics (no valid GB radii). Stick to a PRMTOP built for implicit solvent.

  • barostat: true + implicitsolvent: true errors out. There’s no periodic box, so the barostat setup raises at startup.

  • Inflated diffusion. Diffusion coefficients are higher in implicit solvent because there’s no viscous drag from explicit water. Useful for conformational sampling; not for kinetic / transport quantities.

See also#