gauss

mdhelper.openmm.pair.gauss(cutoff: float | Quantity, cutoff_gauss: float | Quantity = None, *, shift: bool = True, mix: str = 'geometric', global_params: dict[str, float | Quantity] = None, per_params: list = None, tab_funcs: dict[str, ndarray[int | float] | Quantity | Discrete2DFunction] = None) → CustomNonbondedForce

Implements the generalized intermolecular Gaussian pair potential.

The potential energy between two Gaussian particles is given by

\[u_\mathrm{Gauss}(r_{12})=\alpha_{12}\exp{(-\beta_{12}r_{12}^2)}\]

where \(\alpha_{12}\) is a magnitude scaling constant in \(\mathrm{kJ/mol}\) and \(\beta_{12}\) is a screening length in \(\mathrm{nm}\).

In addition to arithmetic and geometric mixing rules for \(\alpha_{12}\) and \(\beta_{12}\), an implementation of the excluded volume pair potential in the Gaussian core model

\[u_\mathrm{Gauss}(r_{12})=A\left(\frac{3}{2\pi\sigma_{12}^2} \right)^{3/2}\exp{\left(-\frac{3}{2\sigma_{12}^2}r_{12}^2\right)}\]

is available, where \(A\) is the repulsion parameter in \(\mathrm{nm}^3\cdot\mathrm{kJ/mol}\) and \(\sigma_{12}\) is the average particle size in \(\mathrm{nm}\).

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_gaussfloat or openmm.unit.Quantity, optional

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

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

shiftbool, keyword-only, default: True

Determines whether the Gaussian potential is shifted at its cutoff to \(0\,\mathrm{kJ/mol}\).

mixstr, keyword-only, default: "geometric"

Mixing rule for \(\alpha_{12}\) and \(\beta_{12}\).

Valid values:

• "arithmetic": Arithmetic combining rule.

  \[\begin{split}\begin{gather*} \alpha_{12}=\sqrt{\alpha_1\alpha_2}\\ \beta_{12}=\frac{2}{\beta_1^{-1}+\beta_2^{-1}} \end{gather*}\end{split}\]

  Per-particle parameters: \((\alpha_i,\,\beta_i)\).

• "geometric": Geometric mixing rule.

  \[\begin{split}\begin{gather*} \alpha_{12}=\sqrt{\alpha_1\alpha_2}\\ \beta_{12}=\sqrt{\beta_1\beta_2} \end{gather*}\end{split}\]

  Per-particle parameters: \((\alpha_i,\,\beta_i)\).

• "core": Gaussian core model.

  \[\begin{split}\begin{gather*} \sigma_{12}^2=\sigma_1^2+\sigma_2^2\\ \beta_{12}=\frac{3}{2\sigma_{12}^2}\\ \alpha_{12}=A\left( \frac{\beta_{12}}{\pi}\right)^{3/2} \end{gather*}\end{split}\]

  Global parameter: \(A\).

  Per-particle parameter: \(\sigma_i\).

• "alpha12 = ...; beta12 = ...;": Custom mixing rule. The string containing the expressions for \(\alpha_{12}\) and \(\beta_{12}\) 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

Optional global parameters for use in the definition of \(\alpha_{12}\) and \(\beta_{12}\).

per_paramslist, keyword-only, optional

Optional per-particle parameters for use in the definition of \(\alpha_{12}\) and \(\beta_{12}\).

tab_funcsdict, keyword-only, optional

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

Returns:

pair_gaussopenmm.CustomNonbondedForce

Gaussian pair potential.