CV:CNGSW: Difference between revisions
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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV: | Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNGSW]] | ||
---- | ---- | ||
{{CVS}} | {{CVS}} | ||
===Definition=== | ===Definition=== | ||
The | The coordination number of central point '''A''' with respect to atoms of the group '''B''' using a switch function. | ||
<center><math>\xi = \sum_{i | <center><math>\xi = \sum_{i=1}^{group_B} \left( 1 - 2 \left( \frac { d_{iA} } { d_{cut} } \right)^2 + \left( \frac {d_{iA}}{d_{cut}} \right)^4 \right) </math></center> | ||
'''PBC note:''' The minimum-image convention is apllied to | <center><math>d_{iA} = | \bold x_i - \bold A_{com} | </math></center> | ||
'''PBC note:''' The minimum-image convention is apllied to distances d<sub>iA</sub> if the [[General setup|fenable_pbc]] option is activated. The convention is not used to calculate the center of mass of the pont '''A'''. It is therefore required that atoms within a group are either covalently bound or are part of complex that will not be separated or reimaged during a simulation. | |||
===Specification=== | ===Specification=== | ||
Section name: ''' | Section name: '''CNGSW''' | ||
{| | {| | ||
| style="width: 5em;" | '''Key''' | | style="width: 5em;" | '''Key''' | ||
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| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atoms specifying the | | atoms specifying the point A | ||
|- | |- | ||
| '''group_b''' | | '''group_b''' | ||
Latest revision as of 15:10, 9 June 2015
Navigation: Documentation / Collective Variables / CV:CNGSW
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Definition
The coordination number of central point A with respect to atoms of the group B using a switch function.
PBC note: The minimum-image convention is apllied to distances diA if the fenable_pbc option is activated. The convention is not used to calculate the center of mass of the pont A. It is therefore required that atoms within a group are either covalently bound or are part of complex that will not be separated or reimaged during a simulation.
Specification
Section name: CNGSW
| Key | Type | Default | Description |
| name | string | unique CV name | |
| group_a | mask | atoms specifying the point A | |
| group_b | mask | atoms specifying the group B | |
| cutoff | real | cut-off distance dcut |
Keys in bold are mandatory.