CV:NABEND: Difference between revisions
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===Definition=== | ===Definition=== | ||
This CV provides dihedral angle between three vectors. Two vectors are defined as z-axes of two reference frames superimposed to the atom groups '''A''' and '''B''', see [[CV:AXANG2]], and the hinge vector is defined by groups '''C''' and '''D'''. | This CV provides dihedral angle between three vectors. Two vectors are defined as z-axes of two reference frames superimposed to the atom groups '''A''' and '''B''', see [[CV:AXANG2]], and the hinge vector is defined by difference between two COMs calculated from groups '''C''' and '''D'''. | ||
'''PBC note:''' The minimum-image convention is not used. | '''PBC note:''' The minimum-image convention is not used. | ||
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| name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_b''' | | name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_b''' | ||
|- | |||
| '''group_c''' | |||
| [[Mask format|mask]] | |||
| | |||
| atoms specifying the point '''C''' | |||
|- | |||
| '''group_d''' | |||
| [[Mask format|mask]] | |||
| | |||
| atoms specifying the point '''D''' | |||
|} | |} | ||
''Keys in bold are mandatory.'' | ''Keys in bold are mandatory.'' | ||
Latest revision as of 17:24, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NABEND
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Definition
This CV provides dihedral angle between three vectors. Two vectors are defined as z-axes of two reference frames superimposed to the atom groups A and B, see CV:AXANG2, and the hinge vector is defined by difference between two COMs calculated from groups C and D.
PBC note: The minimum-image convention is not used.
Specification
Section name: NABEND
| Key | Type | Default | Description |
| name | string | unique CV name | |
| group_a | mask | atoms employed in the superimposition of the reference frame A | |
| reference_a | string | name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a | |
| group_b | mask | atoms employed in the superimposition of the reference frame B | |
| reference_b | string | name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_b | |
| group_c | mask | atoms specifying the point C | |
| group_d | mask | atoms specifying the point D |
Keys in bold are mandatory.