CV:NAPBO: Difference between revisions
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Primitive definition of base pair opening for the A:B base pair defined as a dihedral angle between three vectors: base A vector (C and D points), helical axis vector (A and B points), and base B vector (E and F points). This CV should provide the same value as [[CV:DIH2]] but with the different order of atom groups. | Primitive definition of base pair opening for the A:B base pair defined as a dihedral angle between three vectors: base A vector (C and D points), helical axis vector (A and B points), and base B vector (E and F points). This CV should provide the same value as [[CV:DIH2]] but with the different order of atom groups. | ||
''' | '''NOTE:''' This CV is not well tested. | ||
Latest revision as of 17:17, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NAPBO
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Definition
Primitive definition of base pair opening for the A:B base pair defined as a dihedral angle between three vectors: base A vector (C and D points), helical axis vector (A and B points), and base B vector (E and F points). This CV should provide the same value as CV:DIH2 but with the different order of atom groups.
NOTE: This CV is not well tested.
Specification
Section name: NAPBO
| Key | Type | Default | Description |
| name | string | unique CV name | |
| group_a | mask | atoms specifying the point A | |
| group_b | mask | atoms specifying the point B | |
| group_c | mask | atoms specifying the point C | |
| group_d | mask | atoms specifying the point D | |
| group_e | mask | atoms specifying the point E | |
| group_f | mask | atoms specifying the point F |
Keys in bold are mandatory.