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Build Configuration

Source code:

  • bff/workflows/build/config.py
  • bff/workflows/build/main.py
  • bff/topology.py

Purpose

bff build prepares equilibrated systems and runs one seeded production trajectory for each system. bff prepare-assets packages that seed into FFMD and CP2K reference assets.

  • equilibrated GROMACS systems under equilibration/
  • seeded production outputs under equilibration/system-XXX-prod.*
  • a build-manifest.yaml handoff file consumed by asset-preparation workflows

Minimal Example

project:
  directory: ./
  log: ./out.log

gromacs:
  command: gmx

defaults:
  nsteps:
    npt: 0
    prod: 100000

systems:
  - topology: ../inputs/common/topol.top
    templates:
      ACE: ../inputs/common/ace.gro
    mdp:
      em: ../inputs/common/mdp/em.mdp
      npt: ../inputs/common/mdp/npt.mdp
      prod: ../inputs/common/mdp/nvt.mdp
    charge: -1
    multiplicity: 1
    box: [15.7107, 15.7107, 15.7107, 90, 90, 90]

Top-Level Keys

  • project Project output settings. A string is accepted as shorthand for project.directory.
  • project.directory Output directory for equilibration/ and build-manifest.yaml.
  • project.log Optional workflow log file.
  • gromacs.command GROMACS executable, usually gmx.
  • defaults.nsteps.npt Default NpT equilibration length for systems that do not override it.
  • defaults.nsteps.prod Default seeded production run length for systems that do not override it.
  • systems Non-empty list of systems to build.

systems[] Keys

  • topology GROMACS topology describing residue counts.
  • templates Optional mapping from residue name to coordinate template file for non-standard residues. Omit it when the system only contains built-in water or monoatomic-ion residues.
  • charge Total system charge for staged CP2K reference inputs.
  • multiplicity Spin multiplicity for staged CP2K reference inputs.
  • box Optional box dimensions. Accepts 3 values or full 6-value triclinic format.
  • bias Optional opaque bias specification. Use either plumed_file or colvars_file.
  • nsteps.npt Optional per-system NpT override.
  • nsteps.prod Optional per-system seeded production run length. The seed trajectory is used later by bff prepare-assets.
  • mdp.em Energy minimization MDP file.
  • mdp.npt NpT equilibration MDP file.
  • mdp.prod Production MDP file used for the seeded run and downstream FFMD assets.

Outputs

The main downstream output is PROJECT/build-manifest.yaml. It records the prepared topology, index, MDP files, copied bias input, seeded production coordinate file, seeded production trajectory, CP2K charge/multiplicity, and box for each system.

After a successful build, run bff prepare-assets to write the ffmd/ and reference/ asset trees.