Collective Variables
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Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Collective variables (CVs) define a subset of configuration space in which free energy is being calculated.
The CV definition can be read either from the input file or from an external file. The mode will depend on configuration in the [files] section. If the value of the fcvsdef key contains the name of the group (e.g. string starting with the "{" character) then the CV definition will be read from this group in the input file. Otherwise, the CV definition will be read from a file with the name provided by the fcvsdef key. In the latter case, the CV definition must be in the {MAIN} group (which is implicit and can be omitted in the file).
The group or file can contain several collective variables. Each collective variable is specified in a single section. The name of the section defines a type of CV. The section contains the name key containing a unique CV name and other keys specific to a given CV type.
Extra documentation:
Supported Types
Distance | |||
Type | Description | Type | Description |
DD | distance difference | DIS | distance between two points |
MDIS | minimum value of atom pair distances | MDISG | minimum distance between two atom groups |
ODIS | distance between plane and point | ||
OPOS | absolute position in the oriented coordinate system | OPOS2 | absolute position in the superimposed coordinate system |
ORAD | radial distance in the oriented coordinate system | ORAD2 | radial distance in the superimposed coordinate system |
POS | absolute position | RAD | radial distance |
Angle | |||
Type | Description | Type | Description |
ANG | angle among three points | ANG2 | angle between two vectors defined by four points |
AXANG | angle between two principal axes | AXANG2 | angle between two reference axes |
DIH | dihedral angle among four points | DIH2 | dihedral angle among three vectors defined by six points |
PANG | angle between two planes | PVANG | angle between plane and vector |
Coordination Numbers | |||
Type | Description | Type | Description |
CNFF | coordination number atom-atom using Fermi like function | CNGFF | coordination number point-atom using Fermi like function |
CNSW | coordination number atom-atom using switch function | CNGSW | coordination number point-atom using switch function |
CNRF | coordination number atom-atom using rational function | CNGRF | coordination number point-atom using rational function |
Shape | |||
Type | Description | Type | Description |
ACYL | acylindricity | PMGTD | difference of two principal moments of gyration tensor |
ASPH | asphericity | PMOGT | principal moment of gyration tensor |
SANIS | relative shape anisotropy | RMSDT | root-mean square deviation to target structure |
RGYR | radius of gyration | PLANE | root-mean-square deviation from the plane |
EVEC | projection into essential vector | ||
Nucleic Acids | |||
Type | Description | Type | Description |
NALBPP | local base-pair parameters | NALSTP | local base-pair step parameters |
NASBPP | simple base-pair parameters | NASSTP | simple base-pair step parameters |
NASBPPOLD | simple base-pair parameters | NASSTPOLD | simple base-pair step parameters |
NASBO | simple base-pair opening | NAPBO | primitive base-pair opening |
NABEND | nucleic acid bending | ||
Ring Puckering | |||
Type | Description | Type | Description |
PUCK6Q | total puckering amplitude of six-membered ring | PUCK5Q | total puckering amplitude of five-membered ring |
PUCK6P | puckering azimuthal angle of the six-membered ring | PUCK5P | puckering azimuthal angle of the five-membered ring |
PUCK6T | puckering polar angle of the six-membered ring | ||
Special | |||
Type | Description | Type | Description |
WORMPOS | parametrical position of an axle inside a macrocycle | WORMANG | orientation of an axle inside a macrocycle |
Energy | |||
Type | Description | Type | Description |
POT | potential energy | EGAP | energy gap between two resonance states |
Algebra | |||
Type | Description | Type | Description |
ADD | sum of two collective variables | SUB | difference between two collective variables |
MULT | product of two collective variables | DIV | ratio of two collective variables |
FSWITCH | Fermi-like switch function | RSWITCH | rational switch function |