Enhanced Sampling with PLUMED

SPARC integrates PLUMED as an auxiliary calculator for both AIMD and ML-MD, enabling biased sampling to explore regions of configuration space that plain MD would rarely visit.

PLUMED can be enabled independently for each MD stage in input.yaml:

# Enable for AIMD (Stage 1)
aimd_setup:
  plumed:
    enabled: true
    plumed_file: "plumed_dft.dat"
    kT: 0.02585        # 300 K in eV
    restart: false

# Enable for ML-MD (Stage 3)
mlip_setup:
  plumed:
    enabled: true
    plumed_file: "plumed.dat"
    kT: 0.02585
    restart: false

Any PLUMED collective variable or bias can be used

Because SPARC simply attaches PLUMED as an auxiliary calculator, any collective variable or enhanced sampling method supported by your PLUMED installation can be used — metadynamics, umbrella sampling, steered MD, free energy perturbation, etc.

The Tutorial shows one specific example using SPRINT coordinates with Parallel Bias Metadynamics (PBMetaD) for reactive sampling of the NH₃BH₃ system. This combination worked well for that case, but it is not a requirement — choose the collective variables and bias that suit your system.

Example: SPRINT coordinates

SPRINT (Social PeRmutatIon iNvarianT) coordinates are graph-based collective variables derived from a contact matrix. They:

Are permutation-invariant (atom relabelling does not change the coordinate)
Discriminate chemical environments without prior knowledge of reaction paths
Generalise across bond-breaking and bond-forming events

By definition, SPRINT coordinates are computed from the largest eigenvalue \(\lambda\) of the \(n \times n\) adjacency matrix and its corresponding eigenvector \(\mathbf{V}\):

\[s_i = \sqrt{n} \, \lambda \, v_i\]

Note

SPRINT is part of the adjmat PLUMED module and requires PLUMED to be compiled with --enable-modules=all. See SPARC Installation Guide for instructions.

Tip

See the Tutorial for a complete plumed_dp.dat input file using SPRINT + PBMetaD on the NH₃BH₃ system.

Umbrella sampling

SPARC also supports umbrella sampling windows for free-energy calculations. Enable via:

mlip_setup:
  plumed:
    enabled: true
    plumed_file: "plumed.dat"
    umbrella_sampling:
      enabled: true
      config_file: "umbrella_sampling.yaml"

See Plumed for technical details on the PLUMED wrapper module.