Collective Variables
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Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Collective variables (CVs) define subset of configuration space in which the free energy is being calculated.
The CV definition can be read either from the input file or from an external file. The mode used will depend on set-up in [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 set-up will be read from this group in the input file. Otherwise the CV set-up is read from a file with the name provided by the fcvsdef key. In the later case, CV definition must be in {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 section defines type of CV. The section contains the name key containing a unique CV name and other keys specific for a given CV type.
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 oriented coordinate system |
| ORAD | radial distance in oriented coordinate system | POS | absolute position |
| RAD | radial distance | ||
| Angle | |||
| Type | Description | Type | Description |
| ANG | angle among three points | AXANG | angle between two axes |
| DIH | dihedral angle among four 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 plane |
| EVEC | projection into esential vector | ||
| 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 six-membered ring | PUCK5P | puckering azimuthal angle of five-membered ring |
| PUCK6T | puckering polar angle of six-membered ring | ||
| 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 |