From c04de5151e452a9641a28f1cb0d7e00d4ee0c944 Mon Sep 17 00:00:00 2001 From: bc118 Date: Sun, 8 Oct 2023 19:40:28 -0400 Subject: [PATCH] changed the example variables from override_VDWGeometricSigma to VDWGeometricSigma --- ..._a_dihedral_with_Gaussian_and_write_all_files.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst b/docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst index a8351ac..49bbb33 100644 --- a/docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst +++ b/docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst @@ -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. @@ -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, @@ -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. @@ -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,