This module helps with the definition of CVs in SPONGE
¶ subpackages
¶ submodules
¶ functions
¶ to_string
convert this information to a string
¶ to_string
convert this information to a string
¶ to_string
convert this information to a string
¶ classes
¶ CVSystem
This class is used to help with the definition of CVs in SPONGE
| parameters |
explanation |
| molecule |
the molecule to define the CVs |
the MDAnalysis.Universe of the molecule
¶ id2index
the MDAnalysis.Universe of the molecule
¶ get_atom_index
Convert an Xponge.Atom to int
¶ remove
Remove a name from the system
¶ add_center
Add a virtual atom with the type of "center" to the system
| parameters |
explanation |
| name |
the name of the virtual atom |
| select |
a selection string of MDAnalysis |
| weight |
weight of the atoms, None for 1/N |
¶ add_cv_position
Add a CV with the type of "position" to the system
| parameters |
explanation |
| name |
the name of the CV |
| atom |
an int or a name of virtual atom |
| xyz |
the axis of the position |
| scaled |
whether the posithion need to be scaled |
¶ add_cv_distance
Add a CV with the type of "distance" to the system
| parameters |
explanation |
| name |
the name of the CV |
| atom1 |
an int or a name of virtual atom |
| atom2 |
an int or a name of virtual atom |
¶ add_cv_displacement
Add a CV with the type of "displacement" to the system
| parameters |
explanation |
| name |
the name of the CV |
| atom1 |
an int or a name of virtual atom |
| atom2 |
an int or a name of virtual atom |
| xyz |
the axis of the position |
¶ add_cv_box_length
Add a CV with the type of "box_length" to the system
| parameters |
explanation |
| name |
the name of the CV |
| xyz |
the axis of the position |
¶ add_cv_density
Add a CV with the type of "combination" to the system, which gives the density of the system
| parameters |
explanation |
| name |
the name of the CV |
¶ add_cv_angle
Add a CV with the type of "angle" to the system
| parameters |
explanation |
| name |
the name of the CV |
| atom1 |
an int or a name of virtual atom |
| atom2 |
an int or a name of virtual atom |
| atom3 |
an int or a name of virtual atom |
¶ add_cv_dihedral
Add a CV with the type of "dihedral" to the system
| parameters |
explanation |
| name |
the name of the CV |
| atom1 |
an int or a name of virtual atom |
| atom2 |
an int or a name of virtual atom |
| atom3 |
an int or a name of virtual atom |
| atom4 |
an int or a name of virtual atom |
¶ add_cv_rmsd
Add a CV with the type of "displacement" to the system
| parameters |
explanation |
| name |
the name of the CV |
| select |
a string of selection |
¶ print
Add a CV to print
| parameters |
explanation |
| name |
the name of the CV |
¶ steer
Add a CV to steer
| parameters |
explanation |
| name |
the name of the CV |
| weight |
the weight for steering |
¶ restrain
Add a CV to restrain
| parameters |
explanation |
| name |
the name of the CV |
| weight |
the weight for restraints |
| reference |
the reference for restraints |
| start_step |
the step to start the restraints |
| max_step |
the step to reach the max weight of restraints |
| max_step |
the step to reduce the weight of restraints |
| stop_step |
the step to stop the restraints |
Add a CV to do metadynamics
| parameters |
explanation |
| name |
the name of the CV |
| dCV |
the weight for meta1d |
| CV_minimal |
the minimal value of the CV |
| CV_maximum |
the maximum value of the CV |
| welltemp_factor |
the welltemfactor value of the CV |
| height |
the height of the Gaussian potential to add |
| sigma |
the sigma of the Gaussian potential to add |
¶ output
Output the recorded system to a file
| parameters |
explanation |
| filename |
the name of the output file for cv_in_file |
| folder |
the folder of the output files, the current working folder for default |
