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Changed the example variables from override_VDWGeometricSigma to VDWGeometricSigma #30

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Oct 8, 2023
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Changed the example variables from override_VDWGeometricSigma to VDWGeometricSigma #30

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12 changes: 6 additions & 6 deletions ...etting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,10 @@ Select the desired variables, file, and set the temperature.
# The temperature of the Molecular Mechanics (MM) simulation.
temperature_in_unyt_units = 298.15 * u.Kelvin

# Choose mixing rule (override_VDWGeometricSigma_bool) to override the value (True or False)
# Choose mixing rule (VDWGeometricSigma_bool) to override the value (True or False)
# that was chosen in the force field (FF) XML file. This variable is not required and will be
# selected automatically; however, you should override it if you are unsure of the setting.
override_VDWGeometricSigma_bool = True
VDWGeometricSigma_bool = True

# Atom type naming convention ( str, optional, default=’all_unique’, (‘general’ or ‘all_unique’) )
# General is safe and recommended since we are using a single FF XML file.
Expand Down Expand Up @@ -78,7 +78,7 @@ Run the dihedral fit to fit to the MM simulations:
log_files_and_removed_points,
zeroed_dihedral_atom_types=zeroed_dihedrals,
qm_engine="gaussian",
override_VDWGeometricSigma=override_VDWGeometricSigma_bool,
VDWGeometricSigma=VDWGeometricSigma_bool,
atom_type_naming_style='general',
gomc_cpu_cores=1,
fit_min_validated_r_squared=0.99,
Expand Down Expand Up @@ -120,10 +120,10 @@ Select the desired variables, file, and set the temperature.
# The temperature of the Molecular Mechanics (MM) simulation.
temperature_in_unyt_units = 298.15 * u.Kelvin

# Choose mixing rule (override_VDWGeometricSigma_bool) to override the value (True or False)
# Choose mixing rule (VDWGeometricSigma_bool) to override the value (True or False)
# that was chosen in the force field (FF) XML file. This variable is not required and will be
# selected automatically; however, you should override it if you are unsure of the setting.
override_VDWGeometricSigma_bool = True
VDWGeometricSigma_bool = True

# Atom type naming convention ( str, optional, default=’all_unique’, (‘general’ or ‘all_unique’) )
# General is safe and recommended since we are using a single FF XML file.
Expand Down Expand Up @@ -163,7 +163,7 @@ Run the dihedral fit to fit to the MM simulations:
manual_dihedral_atom_numbers_list=[3, 2, 1, 4],
zeroed_dihedral_atom_types=zeroed_dihedrals,
qm_engine="gaussian_style_final_files",
override_VDWGeometricSigma=override_VDWGeometricSigma_bool,
VDWGeometricSigma=VDWGeometricSigma_bool,
atom_type_naming_style='general',
gomc_cpu_cores=1,
fit_min_validated_r_squared=0.99,
Expand Down
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