solvation

mdhelper.openmm.pair.solvation(cutoff: float | Quantity, cutoff_solvation: float | Quantity = None, *, mix: str = 'arithmetic', per_params: list = None, global_params: dict[str, float | Quantity] = None, tab_funcs: dict[str, ndarray[int | float] | Quantity | Discrete2DFunction] = None) → CustomNonbondedForce[source]

Implements the solvation pair potential.

The solvation energy between particles is given by

\[u_\mathrm{solv}(r_{12})=-S_{12}\left[\left( \frac{\sigma_{12}}{r_{12}}\right)^4 -\left(\frac{\sigma_{12}}{r_\mathrm{cut}}\right)^4\right]\]

where \(\sigma_{12}\) is the size of the particle in \(\mathrm{nm}\) and \(S_{12}\) is the solvation strength in \(\mathrm{kJ/mol}\).

After creating the pair potential, particles should be registered using openmm.openmm.CustomNonbondedForce.addParticle().

Parameters:
cutofffloat or openmm.unit.Quantity

Shared cutoff distance for all nonbonded interactions in the simulation sytem. Must be less than half the minimum periodic simulation box dimension.

Reference unit: \(\mathrm{nm}\).

cutoff_solvationfloat or openmm.unit.Quantity, optional

Cutoff distance \(r_\mathrm{cut}\) for the solvation potential. Must be less than the shared cutoff distance. If not provided, it is set to the shared cutoff distance.

Reference unit: \(\mathrm{nm}\).

mixstr, keyword-only, default: "arithmetic"

Mixing rule for \(\sigma_{12}\) and \(S_{12}\).

Valid values:

  • "arithmetic": Arithmetic mixing rule.

    \[\begin{split}\begin{gather*} \sigma_{12}=\frac{\sigma_1+\sigma_2}{2}\\ S_{12}=\sqrt{S_1S_2} \end{gather*}\end{split}\]

    Per-particle parameters: \((\sigma_i, S_i)\).

  • "geometric": Geometric mixing rule.

    \[\begin{split}\begin{gather*} \sigma_{12}=\sqrt{\sigma_1\sigma_2}\\ S_{12}=\sqrt{S_1S_2} \end{gather*}\end{split}\]

    Per-particle parameters: \((\sigma_i, S_i)\).

  • "sigma12 = ...; S12 = ...;": Custom mixing rule. The string containing the expressions for \(\sigma_{12}\) and \(S_{12}\) must be written in valid C++ syntax, with any custom global and per-particle parameters and tabulated functions defined in global_params, per_params, and tab_funcs, respectively.

global_paramsdict, keyword-only, optional

Additional global parameters for use in the definition of \(\sigma_{12}\) and \(S_{12}\).

per_paramslist, keyword-only, optional

Additional per-particle parameters for use in the definition of \(\sigma_{12}\) and \(S_{12}\).

tab_funcsdict, keyword-only, optional

Optional tabulated functions for use in the definition of \(\sigma_{12}\) and \(S_{12}\).

Returns:
pair_solvopenmm.CustomNonbondedForce

Solvation pair potential.