View source for CV:DD

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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:DD]]
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{{CVS}}
===Definition===
The difference between two distances. Each distance is calculated as a distance between the center of mass of two groups of atoms. 
<center><math>\xi = | \bold A_{com} - \bold B_{com} | - | \bold C_{com} - \bold D_{com} |</math></center>
'''PBC note:''' The minimum-image convention is apllied to the distances |AB| and |CD| only if the [[General setup|fenable_pbc]] option is activated. The convention is not used to calculate the center of mass. 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. The convention is not also applied to the distance difference result.


===Specification===
Section name: '''DD'''
{|
| style="width: 5em;" | '''Key''' 
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|-
| '''group_a'''
| [[Mask format|mask]]
|
| atoms specifying the point '''A'''
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''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.''