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point_charges

Include effects of point charges through electrostatic, and possibly van der Waals, interactions with QM atoms.

Periodic point charge embedding is only compatible with GFN1-xTB and is activated by including the lattice sub-command. This command can appear in the global context.

Subcommands

Options

charges

Charges for each particle defined by xyz

  • The type is [real]
  • There is no default value.
coupling_scheme

Specify the coupling scheme between QM and MM subsystems.

  • The type is string
  • The default is electrostatic
  • The value must be one of:
    • oniom - Use the ONIOM coupling scheme.
    • mechanical - Use the mechanical coupling scheme.
    • electrostatic - Use the electrostatic coupling scheme.
ewald_alpha

Broadening parameter for Gaussian screening of point charges in Ewald treatment of second and third order terms of xTB Hamiltonian. This effectively determines the relative contributions of real-space and reciprocal-space terms in the Ewald sum. As \(\alpha\) is increased, ewald_real_cutoff should be decreased, while ewald_reciprocal_cutoff should be increased. By default, entos determines this from ewald_real_cutoff and ewald_relative_error, using the expression: \( \alpha = \frac{1}{r_c} \bigg[ W \bigg( \frac{Q}{E}\sqrt{\frac{r_c}{2V}} \bigg) \bigg]^{1/2}, \) where \(r_c\) is the ewald_real_cutoff, \(E\) is the ewald_relative_error, \( Q = \sum^{N_{atoms}}_{i=1} q_i^2 \), \(\{q_i\}\) are atomic partial charges of neutral atoms, \(W\) is the Lambert W function, and \(V\) is the system volume. This approximation is not guaranteed to give ideal results, but it works fairly well for most systems. Further details can be found in A comparison of the Spectral Ewald and Smooth Particle Mesh Ewald methods in GROMACS.

  • The type is real
  • There is no default value.
ewald_real_cutoff

Real-space cut-off over unit cells in Ewald sum.

  • The type is quantity
  • There is no default value.
ewald_reciprocal_cutoff

Reciprocal-space cut-off over k-vectors in Ewald sum. By default, entos determines this from ewald_real_cutoff and ewald_relative_error, using the expression: \( k_c = \frac{\sqrt{3} L \alpha}{2 \pi} \bigg[ W \bigg( \frac{4}{3L^2} \bigg(\frac{Q^2}{\pi \alpha E^2}\bigg)^{2/3} \bigg) \bigg]^{1/2} \) where \(\alpha\) is the ewald_alpha, \(E\) is the ewald_relative_error, \( Q = \sum^{N_{atoms}}_{i=1} q_i^2 \), \(\{q_i\}\) are atomic partial charges of neutral atoms, \(W\) is the Lambert W function, and \(L\) is the average system length. This approximation is not guaranteed to give ideal results, but it works fairly well for most systems. Further details can be found in A comparison of the Spectral Ewald and Smooth Particle Mesh Ewald methods in GROMACS.

  • The type is real
  • There is no default value.
file

Specify name of the file containing MM point charges. The format of a point-charge file should be: the first line containing the number of point charges, and each of the remaining lines containing the charge and the xyz coordinates (in Angstrom). For example, the following file specifies three point charges: 3 0.123 0.0000 0.0000 0.0000 -2.345 1.0000 1.0000 0.0000 3.456 -1.0000 -1.0000 0.0000

  • The type is string
  • There is no default value.
xyz

Positions of charges

  • The type is [(real, real, real)]
  • There is no default value.