PMFLib Wiki - User contributions [en]

References

2015-07-21T13:34:29Z

Tbouchal:

<ref name="jmeno_citace"/>

==References==
<references>
<ref name="jmeno_citace">Kumari, M.; Kozmon, S.; Kulhánek, P.; Štepán, J.; Tvaroška, I.; Koča, J. Exploring Reaction Pathways for O -GlcNAc Transferase Catalysis. A String Method Study. ''The Journal of Physical Chemistry B'' '''2015''', ''119 (12)'', 4371–4381, doi: 10.1021/jp511235f.
</ref>
</references>

Ring Puckering

2015-06-15T10:13:10Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]]
----
{{CVS}}__NOEDITSECTION__
[[File:Puckering.png|500px|left|thumb|scheme of ring puckering]]

Ring Puckering

2015-06-15T10:13:00Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]]
----
{{CVS}}__NOEDITSECTION__
[[File:Puckering.png|500px|left|thumb|scheme of ring puckering <ref name="Cremer Pople"/>]]

CV:PUCK5P

2015-06-15T09:08:51Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK5P]]
----
{{CVS}}
===Definition===
Puckering azimuthal angle of five-membered ring is defined as:
<center><math>\xi = q_{\phi} = atan2 \left (\frac{q_y}{q_x} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{5}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>q_x = \sqrt{ \frac{2}{5} } \sum_{i=1}^{5}{z_i cos \left (\frac{4\pi[i-1]}{5} \right )}</math></center>
<center><math>q_y = -\sqrt{ \frac{2}{5} } \sum_{i=1}^{5}{z_i sin \left (\frac{4\pi[i-1]}{5} \right )}</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK5P'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to E.

CV:PUCK5Q

2015-06-15T09:08:32Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK5Q]]
----
{{CVS}}
===Definition===
Total puckering amplitude is defined as:
<center><math>\xi = Q = \sqrt{ \sum_{i=1}^{5}{z_i^2} } </math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{5}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK5Q'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to D.

CV:PUCK6T

2015-06-15T09:08:11Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK6T]]
----
{{CVS}}
===Definition===
Puckering polar angle of six-membered ring is defined as:
<center><math>\xi = q_{\theta} = acos \left (\frac{q_z}{Q} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>Q = \sqrt{ \sum_{i=1}^{6}{z_i^2} } </math></center>
<center><math>q_z = \sqrt{ \frac{1}{6} } \sum_{i=1}^{6}{(-1)^{(i-1)} z_i}</math></center>
'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6T'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

CV:PUCK6P

2015-06-15T09:07:47Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK6P]]
----
{{CVS}}
===Definition===
Puckering azimuthal angle of six-membered ring is defined as:
<center><math>\xi = q_{\phi} = atan2 \left (\frac{q_y}{q_x} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>q_x = \sqrt{ \frac{2}{6} } \sum_{i=1}^{6}{z_i cos \left (\frac{4\pi[i-1]}{6} \right )}</math></center>
<center><math>q_y = -\sqrt{ \frac{2}{6} } \sum_{i=1}^{6}{z_i sin \left (\frac{4\pi[i-1]}{6} \right )}</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6P'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

CV:PUCK6P

2015-06-15T09:07:35Z

Tbouchal:

__NOEDITSECTION__
[[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK6P]]
Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK6P]]
----
{{CVS}}
===Definition===
Puckering azimuthal angle of six-membered ring is defined as:
<center><math>\xi = q_{\phi} = atan2 \left (\frac{q_y}{q_x} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>q_x = \sqrt{ \frac{2}{6} } \sum_{i=1}^{6}{z_i cos \left (\frac{4\pi[i-1]}{6} \right )}</math></center>
<center><math>q_y = -\sqrt{ \frac{2}{6} } \sum_{i=1}^{6}{z_i sin \left (\frac{4\pi[i-1]}{6} \right )}</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6P'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

CV:PUCK6Q

2015-06-15T09:06:49Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]] / [[CV:PUCK6Q]]

----
{{CVS}}
===Definition===
The total puckering amplitude is defined as:
<center><math>\xi = Q = \sqrt{ \sum_{i=1}^{6}{z_i^2} } </math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6Q'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

Ring Puckering

2015-06-15T09:04:59Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]]
----
{{CVS}}__NOEDITSECTION__
[[File:Puckering.png|500px|left|thumb|scheme of ring puckering]]

Ring Puckering

2015-06-15T09:01:04Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]]
----
{{CVS}}__NOEDITSECTION__
[[File:puckering.png|500px|left|thumb|scheme of ring puckering]]

Ring Puckering

2015-06-15T08:54:59Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]]
----
{{CVS}}__NOEDITSECTION__
[[File:puckering.png|900px]]

Ring Puckering

2015-06-15T08:53:42Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]] / [[Ring Puckering]]
----
{{CVS}}__NOEDITSECTION__
[[File:puckering.png]]

CV:EGAP

2015-06-11T13:14:47Z

Tbouchal:

Navigation: [[Documentation]] / [[Collective Variables]]
----
{{CVS}}

CV:POT

2015-06-11T13:14:22Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:POT]]
----
{{CVS}}
===Definition===
The potential energy of the system. This energy does not include the energy of restraints from PMFLib.

<center><math>\xi = E_{pot}</math></center>

===Specification===
Section name: '''POT'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|}
''Keys in bold are mandatory.''

CV:POT

2015-06-11T13:14:12Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective variables]] / [[CV:POT]]
----
{{CVS}}
===Definition===
The potential energy of the system. This energy does not include the energy of restraints from PMFLib.

<center><math>\xi = E_{pot}</math></center>

===Specification===
Section name: '''POT'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|}
''Keys in bold are mandatory.''

CV:CNGSW

2015-06-09T14:10:05Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNGSW]]
----
{{CVS}}
===Definition===
The coordination number of central point '''A''' with respect to atoms of the group '''B''' using a switch function.

<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>

<center><math>d_{iA} = | \bold x_i - \bold A_{com} | </math></center>

'''PBC note:''' The minimum-image convention is apllied to distances diA 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===
Section name: '''CNGSW'''
{|
| 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 group B
|-
| '''cutoff'''
| real
|
| cut-off distance dcut
|}
''Keys in bold are mandatory.''

CV:PLANE

2015-06-09T14:08:41Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PLANE ---- {{CVS}} ===Definition=== The root-mean square distance of atoms to the plane tha..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PLANE]]
----
{{CVS}}
===Definition===
The root-mean square distance of atoms to the plane that is the best fit among them.
<center><math>\xi = \sqrt{ \frac {\sum_{i=1}^{group_A} m_i(\bold n_A . [\bold x_{i} - \bold A_{com}])^2} { \sum_{i=1}^{group_A} m_i} }</math></center>
where '''n'''A is the plane normal vector.

The plane is defined as the best fit among atoms in the atom group '''A'''. The fit is mass weighted.
<center><math>\psi(\bold n_A) = \sum_{i=1}^{group_A}{m_i[\bold n_A .( \bold x_i - \bold A_{com})]^2} \rightarrow min!</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PLANE'''
{|
| 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 plane '''A'''
|}
''Keys in bold are mandatory.''

CV:RMSDT

2015-06-09T14:08:11Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:RMSDT ---- {{CVS}} ===Definition=== The root mean square deviation of the structure fitted..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:RMSDT]]
----
{{CVS}}
===Definition===
The root mean square deviation of the structure fitted to the reference structure. The fit is mass weighted.
<center><math>\xi = \sqrt{ \frac {\sum_{i=1}^{N}{ m_i | \bold R_i^' - \bold R_{ref,i}|^2 }} {\sum_{i=1}^{N}{ m_i}} }</math></center>
where '''R'''' is the structure superimposed onto the reference structure '''R'''ref.

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''RMSDT'''
{|
| 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 involved in the projection
|-
| '''target'''
| 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'''
|}
''Keys in bold are mandatory.''

CV:PMOGT

2015-06-09T14:07:45Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PMOGT ---- {{CVS}} ===Definition=== The selected principal moment of the mass weighted gyra..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PMOGT]]
----
{{CVS}}
===Definition===
The selected principal moment of the mass weighted gyration tensor '''S''' calculated for the atom group '''A'''.

<center><math>\xi = \lambda_n^2</math></center>

where λ is the selected principal moment of the gyration tensor. The mass weighted gyration tensor '''S''' is defined as

<center><math>S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i} </math></center>

The eigenvalues of the tensor are <math>\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2</math>:
<center><math>
\bold S = \begin{bmatrix}
\lambda_{x}^{2} & 0 & 0 \\
0 & \lambda_{y}^{2} & 0 \\
0 & 0 & \lambda_{z}^{2}
\end{bmatrix}
</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PMOGT'''
{|
| 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 group '''A'''
|-
| '''axis'''
| x,y,z
|
| principal moment axis
|}
''Keys in bold are mandatory.''

CV:PMGTD

2015-06-09T14:07:12Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PMGTD ---- {{CVS}} ===Definition=== The difference between two principal moments of the mas..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PMGTD]]
----
{{CVS}}
===Definition===
The difference between two principal moments of the mass weighted gyration tensor '''S''' calculated for the atom group '''A'''.

<center><math>\xi = \lambda_a - \lambda_b</math></center>

where λ are selected principal moments of the gyration tensor. The mass weighted gyration tensor '''S''' is defined as

<center><math>S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i} </math></center>

The eigenvalues of the tensor are <math>\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2</math>:
<center><math>
\bold S = \begin{bmatrix}
\lambda_{x}^{2} & 0 & 0 \\
0 & \lambda_{y}^{2} & 0 \\
0 & 0 & \lambda_{z}^{2}
\end{bmatrix}
</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PMGTD'''
{|
| 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 group '''A'''
|-
| '''axis_a'''
| x,y,z
|
| the principal moment axis ''a''
|-
| '''axis_b'''
| x,y,z
|
| the principal moment axis ''b''
|}
''Keys in bold are mandatory.''

CV:EVEC

2015-06-09T14:06:11Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:EVEC ---- {{CVS}} ===Definition=== The projection of atom configuration onto the essential..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:EVEC]]
----
{{CVS}}
===Definition===
The projection of atom configuration onto the essential vector producing the essential coordinate.
<center><math>\xi = (\bold r^' - \bold r_{a}). \bold v_{e}</math></center>
where '''r'''' is the structure superimposed onto the average structure '''r'''a and '''v'''e is the essential vector.

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''EVEC'''
{|
| 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 involved in the projection
|-
| '''average'''
| string
|
| name of file with the average structure in the XYZ format, the structure must have the same number of atoms as the group '''group_a'''
|-
| '''evec'''
| string
|
| name of file with the essential vector in the format produced by the CATs package
|}
''Keys in bold are mandatory.''

CV:RGYR

2015-06-09T14:05:44Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:RGYR ---- {{CVS}} ===Definition=== The radius of gyration of atoms in the group '''A'''. <c..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:RGYR]]
----
{{CVS}}
===Definition===
The radius of gyration of atoms in the group '''A'''.
<center><math>\xi = \sqrt{ \frac { \sum_{i=1}^{group_A} m_i ( \bold x_i - \bold A_{com}) ^2 } { \sum_{i=1}^{group_A} m_i} }</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''RGYR'''
{|
| 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 group '''A'''
|}
''Keys in bold are mandatory.''

CV:SANIS

2015-06-09T14:05:11Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:SANIS ---- {{CVS}} ===Definition=== The relative shape anisotropy of atoms in the group '''..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:SANIS]]
----
{{CVS}}
===Definition===
The relative shape anisotropy of atoms in the group '''A'''.

<center><math>\xi = \frac { b^2 + \frac{3}{4} c^2 } {R_g^4}</math></center>

where b is the the asphericity, c is the acylindricity, and Rg is the radius of gyration.

<center><math>b = \lambda_z^2 - \frac {1}{2}( \lambda_x^2 + \lambda_y^2 ) </math></center>
<center><math>c = \lambda_y^2 - \lambda_x^2 </math></center>
<center><math>R_g = \lambda_x^2 + \lambda_y^2 + \lambda_z^2</math></center>

where λ are principal moments of the gyration tensor. The mass weighted gyration tensor '''S''' is defined as

<center><math>S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i} </math></center>

The eigenvalues of the tensor are <math>\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2</math>:
<center><math>
\bold S = \begin{bmatrix}
\lambda_{x}^{2} & 0 & 0 \\
0 & \lambda_{y}^{2} & 0 \\
0 & 0 & \lambda_{z}^{2}
\end{bmatrix}
</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''SANIS'''
{|
| 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 group '''A'''
|}
''Keys in bold are mandatory.''

CV:ASPH

2015-06-09T14:04:45Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:ASPH ---- {{CVS}} ===Definition=== The asphericity of atom distribution in the group '''A''..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:ASPH]]
----
{{CVS}}
===Definition===
The asphericity of atom distribution in the group '''A'''. The value is zero when the distribution of atoms is spherically symmetric.

<center><math>\xi = \lambda_z^2 - \frac {1}{2}( \lambda_x^2 + \lambda_y^2 ) </math></center>

where λ are principal moments of the gyration tensor. The mass weighted gyration tensor '''S''' is defined as

<center><math>S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i} </math></center>

The eigenvalues of the tensor are <math>\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2</math>:
<center><math>
\bold S = \begin{bmatrix}
\lambda_{x}^{2} & 0 & 0 \\
0 & \lambda_{y}^{2} & 0 \\
0 & 0 & \lambda_{z}^{2}
\end{bmatrix}
</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''ASPH'''
{|
| 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 group '''A'''
|}
''Keys in bold are mandatory.''

CV:ACYL

2015-06-09T14:03:46Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:ACYL ---- {{CVS}} ===Definition=== The acylindricity of atom distribution in the group '''A..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:ACYL]]
----
{{CVS}}
===Definition===
The acylindricity of atom distribution in the group '''A'''. The value is zero when the distribution of atoms is cylindrically symmetric.

<center><math>\xi = \lambda_y^2 - \lambda_x^2 </math></center>

where λ are principal moments of the gyration tensor. The mass weighted gyration tensor '''S''' is defined as

<center><math>S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i} </math></center>

The eigenvalues of the tensor are <math>\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2</math>:
<center><math>
\bold S = \begin{bmatrix}
\lambda_{x}^{2} & 0 & 0 \\
0 & \lambda_{y}^{2} & 0 \\
0 & 0 & \lambda_{z}^{2}
\end{bmatrix}
</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''ACYL'''
{|
| 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 group '''A'''
|}
''Keys in bold are mandatory.''

CV:PUCK5Q

2015-06-09T14:02:08Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PUCK5Q ---- {{CVS}} ===Definition=== Total puckering amplitude is defined as: <center><math..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PUCK5Q]]
----
{{CVS}}
===Definition===
Total puckering amplitude is defined as:
<center><math>\xi = Q = \sqrt{ \sum_{i=1}^{5}{z_i^2} } </math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{5}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK5Q'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to D.

CV:PUCK5P

2015-06-09T14:01:00Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PUCK5P ---- {{CVS}} ===Definition=== Puckering azimuthal angle of five-membered ring is def..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PUCK5P]]
----
{{CVS}}
===Definition===
Puckering azimuthal angle of five-membered ring is defined as:
<center><math>\xi = q_{\phi} = atan2 \left (\frac{q_y}{q_x} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{5}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{5}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{5} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>q_x = \sqrt{ \frac{2}{5} } \sum_{i=1}^{5}{z_i cos \left (\frac{4\pi[i-1]}{5} \right )}</math></center>
<center><math>q_y = -\sqrt{ \frac{2}{5} } \sum_{i=1}^{5}{z_i sin \left (\frac{4\pi[i-1]}{5} \right )}</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK5P'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to E.

CV:PUCK6Q

2015-06-09T14:00:16Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PUCK6Q ---- {{CVS}} ===Definition=== The total puckering amplitude is defined as: <center><..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PUCK6Q]]
----
{{CVS}}
===Definition===
The total puckering amplitude is defined as:
<center><math>\xi = Q = \sqrt{ \sum_{i=1}^{6}{z_i^2} } </math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6Q'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

CV:PUCK6P

2015-06-09T13:59:45Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PUCK6P ---- {{CVS}} ===Definition=== Puckering azimuthal angle of six-membered ring is defi..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PUCK6P]]
----
{{CVS}}
===Definition===
Puckering azimuthal angle of six-membered ring is defined as:
<center><math>\xi = q_{\phi} = atan2 \left (\frac{q_y}{q_x} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>q_x = \sqrt{ \frac{2}{6} } \sum_{i=1}^{6}{z_i cos \left (\frac{4\pi[i-1]}{6} \right )}</math></center>
<center><math>q_y = -\sqrt{ \frac{2}{6} } \sum_{i=1}^{6}{z_i sin \left (\frac{4\pi[i-1]}{6} \right )}</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6P'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

CV:PUCK6T

2015-06-09T13:58:49Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PUCK6T ---- {{CVS}} ===Definition=== Puckering polar angle of six-membered ring is defined..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PUCK6T]]
----
{{CVS}}
===Definition===
Puckering polar angle of six-membered ring is defined as:
<center><math>\xi = q_{\theta} = acos \left (\frac{q_z}{Q} \right )</math></center>
The centre of the ring is defined as:
<center><math>\bold R_{cog} = \sum_{i=1}^{6}{\bold X_i}</math></center>
Using two helper vectors RI and RII, the ring z-axis n can be defined as:
<center><math>\bold R_{I} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})sin \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold R_{II} = \sum_{i=1}^{6}{(\bold X_i-\bold R_{cog})cos \left (\frac{2\pi[i-1]}{6} \right )}</math></center>
<center><math>\bold n = \frac{\bold R_{I} \times \bold R_{II}}{|\bold R_{I} \times \bold R_{II}|}</math></center>
For every ring atom, the displacement from the mean ring plane is defined as:
<center><math>z_i = \bold n \cdot (\bold X_i-\bold R_{cog})</math></center>
Then two ring-puckering coordinates can be defined as:
<center><math>Q = \sqrt{ \sum_{i=1}^{6}{z_i^2} } </math></center>
<center><math>q_z = \sqrt{ \frac{1}{6} } \sum_{i=1}^{6}{(-1)^{(i-1)} z_i}</math></center>
'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PUCK6T'''
{|
| 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''', only one atom can be within the group
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', only one atom can be within the group
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', only one atom can be within the group
|-
| '''group_d'''
| [[Mask format|mask]]
|
| atoms specifying the point '''D''', only one atom can be within the group
|-
| '''group_e'''
| [[Mask format|mask]]
|
| atoms specifying the point '''E''', only one atom can be within the group
|-
| '''group_f'''
| [[Mask format|mask]]
|
| atoms specifying the point '''F''', only one atom can be within the group
|}
''Keys in bold are mandatory.'' Ring atoms should be specified in the sequence from A to F.

CV:EGAP

2015-06-09T13:55:32Z

Tbouchal: Created page with "Navigation: Documentation / Collective variables ---- {{CVS}}"

Navigation: [[Documentation]] / [[Collective variables]]
----
{{CVS}}

CV:POT

2015-06-09T13:54:22Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / User documentation / CV:POT ---- {{CVS}} ===Definition=== The potential energy of the system. This energy does not in..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[User documentation]] / [[CV:POT]]
----
{{CVS}}
===Definition===
The potential energy of the system. This energy does not include the energy of restraints from PMFLib.

<center><math>\xi = E_{pot}</math></center>

===Specification===
Section name: '''POT'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique CV name
|}
''Keys in bold are mandatory.''

CV:ADD

2015-06-09T13:53:01Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:ADD ---- {{CVS}} ===Definition=== The sum of two collective variables. <center><math>\xi =..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:ADD]]
----
{{CVS}}
===Definition===
The sum of two collective variables.
<center><math>\xi = \xi_{left} + \xi_{right}</math></center>

===Specification===
Section name: '''ADD'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique name of resulting CV
|-
| '''left'''
| string
|
| name of left CV, the CV must be already defined
|-
| '''right'''
| string
|
| name of right CV, the CV must be already defined
|}
''Keys in bold are mandatory.''

CV:MULT

2015-06-09T13:52:36Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:MULT]]
----
{{CVS}}
===Definition===
The product of two collective variables.
<center><math>\xi = \xi_{left} * \xi_{right}</math></center>

===Specification===
Section name: '''MULT'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique name of resulting CV
|-
| '''left'''
| string
|
| name of left CV, the CV must be already defined
|-
| '''right'''
| string
|
| name of right CV, the CV must be already defined
|}
''Keys in bold are mandatory.''

CV:SUB

2015-06-09T13:52:17Z

Tbouchal:

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:SUB]]
----
{{CVS}}
===Definition===
The differnece between two collective variables.
<center><math>\xi = \xi_{left} - \xi_{right}</math></center>

===Specification===
Section name: '''SUB'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique name of resulting CV
|-
| '''left'''
| string
|
| name of left CV, the CV must be already defined
|-
| '''right'''
| string
|
| name of right CV, the CV must be already defined
|}
''Keys in bold are mandatory.''

CV:SUB

2015-06-09T13:52:05Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective variables / CV:SUB ---- {{CVS}} ===Definition=== The differnece between two collective variables. <center..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective variables]] / [[CV:SUB]]
----
{{CVS}}
===Definition===
The differnece between two collective variables.
<center><math>\xi = \xi_{left} - \xi_{right}</math></center>

===Specification===
Section name: '''SUB'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique name of resulting CV
|-
| '''left'''
| string
|
| name of left CV, the CV must be already defined
|-
| '''right'''
| string
|
| name of right CV, the CV must be already defined
|}
''Keys in bold are mandatory.''

CV:MULT

2015-06-09T13:51:19Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective variables / CV:MULT ---- {{CVS}} ===Definition=== The product of two collective variables. <center><math>..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective variables]] / [[CV:MULT]]
----
{{CVS}}
===Definition===
The product of two collective variables.
<center><math>\xi = \xi_{left} * \xi_{right}</math></center>

===Specification===
Section name: '''MULT'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique name of resulting CV
|-
| '''left'''
| string
|
| name of left CV, the CV must be already defined
|-
| '''right'''
| string
|
| name of right CV, the CV must be already defined
|}
''Keys in bold are mandatory.''

CV:DIV

2015-06-09T13:50:51Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:DIV ---- {{CVS}} ===Definition=== The ratio between two collective variables. <center><mat..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:DIV]]
----
{{CVS}}
===Definition===
The ratio between two collective variables.
<center><math>\xi = \xi_{left} / \xi_{right} = \frac{\xi_{left}}{\xi_{right}}</math></center>

===Specification===
Section name: '''DIV'''
{|
| style="width: 5em;" | '''Key'''
| style="width: 5em;" | '''Type'''
| style="width: 5em;" | '''Default'''
| '''Description'''
|-
|<hr/> || <hr/> || <hr/> || <hr/>
|-
| '''name'''
| string
|
| unique name of resulting CV
|-
| '''left'''
| string
|
| name of left CV, the CV must be already defined
|-
| '''right'''
| string
|
| name of right CV, the CV must be already defined
|}
''Keys in bold are mandatory.''

CV:CNGRF

2015-06-09T13:47:26Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:CNGRF ---- {{CVS}} ===Definition=== The coordination numbers of the point '''A''' with resp..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNGRF]]
----
{{CVS}}
===Definition===
The coordination numbers of the point '''A''' with respect to atoms of the group '''B''' using a rational function.

<center><math>\xi = \sum_{i=1}^{group_B} \frac{ 1 - \left( \frac{d_{iA} - d_{offset}}{d_{o}} \right) ^ n }{ 1 - \left( \frac{d_{iA}- d_{offset}}{d_{o}} \right) ^ m } </math></center>

<center><math>d_{iA} = | \bold x_i - \bold A_{com} | </math></center>

'''PBC note:''' The minimum-image convention is apllied to distances diA 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===
Section name: '''CNGRF'''
{|
| 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 group B
|-
| '''offset'''
| real
|
| the value of doffset
|-
| '''reference'''
| real
|
| the reference distance d0
|-
| '''npower'''
| integer
|
| the value of n-power
|-
| '''mpower'''
| integer
|
| the value of m-power
|}
''Keys in bold are mandatory.''

CV:CNRF

2015-06-09T13:45:05Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:CNRF ---- {{CVS}} ===Definition=== The sum of coordination numbers of atoms from the group..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNRF]]
----
{{CVS}}
===Definition===
The sum of coordination numbers of atoms from the group '''A''' with respect to atoms of the group '''B''' using a rational function.

<center><math>\xi = \sum_{i=1}^{group_A} \sum_{j=1}^{group_B} \frac{ 1 - \left( \frac{d_{ij} - d_{offset}}{d_{o}} \right) ^ n }{ 1 - \left( \frac{d_{ij}- d_{offset}}{d_{o}} \right) ^ m } </math></center>

'''PBC note:''' The minimum-image convention is apllied to all atom pair distances if the [[General setup|fenable_pbc]] option is activated.

===Specification===
Section name: '''CNRF'''
{|
| 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 group A
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the group B
|-
| '''offset'''
| real
|
| the value of doffset
|-
| '''reference'''
| real
|
| the reference distance d0
|-
| '''npower'''
| integer
|
| the value of n-power
|-
| '''mpower'''
| integer
|
| the value of m-power
|}
''Keys in bold are mandatory.''

CV:CNGSW

2015-06-09T13:44:07Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:CNSW ---- {{CVS}} ===Definition=== The sum of coordination numbers of atoms from the group..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNSW]]
----
{{CVS}}
===Definition===
The sum of coordination numbers of atoms from the group '''A''' with respect to atoms of the group '''B''' using a switch function.

<center><math>\xi = \sum_{i=1}^{group_A} \sum_{j=1}^{group_B} \left( 1 - 2 \left( \frac { d_{ij} } { d_{cut} } \right)^2 + \left( \frac {d_{ij}}{d_{cut}} \right)^4 \right) </math></center>

'''PBC note:''' The minimum-image convention is apllied to all atom pair distances if the [[General setup|fenable_pbc]] option is activated.

===Specification===
Section name: '''CNSW'''
{|
| 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 group A
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the group B
|-
| '''cutoff'''
| real
|
| cut-off distance dcut
|}
''Keys in bold are mandatory.''

CV:CNSW

2015-06-09T13:42:36Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:CNSW ---- {{CVS}} ===Definition=== The sum of coordination numbers of atoms from the group..."

CV:CNGFF

2015-06-09T13:41:25Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:CNGFF ---- {{CVS}} ===Definition=== The coordination number of central point '''A''' with r..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNGFF]]
----
{{CVS}}
===Definition===
The coordination number of central point '''A''' with respect to atoms of the group '''B''' using a Fermi-like function.

<center><math>\xi = \sum_{i=1}^{group_B} \frac{1}{ 1 + e^{ \beta (d_{iA} - d_{0}) } } </math></center>

<center><math>d_{iA} = | \bold x_i - \bold A_{com} | </math></center>

'''PBC note:''' The minimum-image convention is apllied to distances diA 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===
Section name: '''CNGFF'''
{|
| 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 group B
|-
| '''steepness'''
| real
|
| factor β
|-
| '''reference'''
| real
|
| reference distance d0
|}
''Keys in bold are mandatory.''

CV:CNFF

2015-06-09T13:40:35Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:CNFF ---- {{CVS}} ===Definition=== The sum of coordination numbers of atoms from the group..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:CNFF]]
----
{{CVS}}
===Definition===
The sum of coordination numbers of atoms from the group '''A''' with respect to atoms of the group '''B''' using a Fermi-like function.

<center><math>\xi = \sum_{i=1}^{group_A} \sum_{j=1}^{group_B} \frac{1}{ 1 + e^{ \beta (d_{ij} - d_{0}) } } </math></center>

'''PBC note:''' The minimum-image convention is apllied to all atom pair distances if the [[General setup|fenable_pbc]] option is activated.

===Specification===
Section name: '''CNFF'''
{|
| 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 group A
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the group B
|-
| '''steepness'''
| real
|
| factor β
|-
| '''reference'''
| real
|
| reference distance d0
|}
''Keys in bold are mandatory.''

CV:PVANG

2015-06-09T13:31:14Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PVANG ---- {{CVS}} ===Definition=== The angle between the normal vector of the plane '''A''..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PVANG]]
----
{{CVS}}
===Definition===
The angle between the normal vector of the plane '''A''' and the vector pointing from the point '''B''' to the point '''C'''.

<center><math>\xi = arccos \left(\frac{ \bold n_A . ( \bold C_{com} - \bold B_{com} )}{ | \bold C_{com} - \bold B_{com} |} \right)</math></center>

The plane is defined as the best fit among atoms in the atom group '''A'''. The fit is mass weighted.
<center><math>\psi(\bold n_A^') = \sum_{i=1}^{group_A}{m_i[\bold n_A^' .( \bold x_i - \bold A_{com})]^2} \rightarrow min!</math></center>

The orientation of the plane normal vector is controled by two helper vectors '''x'''dir and '''y'''dir:
<center><math>\bold n_A = sign( \bold n_A^' . (\bold x_{dir} \times \bold y_{dir}) ) \bold n_A^'</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PVANG'''
{|
| 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 plane '''A'''
|- style="vertical-align: top;"
| '''x_direction'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate x-direction vector. The vector origin is in '''A'''com. The atom must be member of the group '''A'''.
|- style="vertical-align: top;"
| '''y_direction'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate y-direction vector. The vector origin is in '''A'''com. The atom must be member of the group '''A'''.
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the point '''B''', which is the origin of the vector
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying the point '''C''', which is the end of the vector
|}
''Keys in bold are mandatory.''

CV:PANG

2015-06-09T13:29:13Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:PANG ---- {{CVS}} ===Definition=== The angle between two normal plane vectors. <center><ma..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:PANG]]
----
{{CVS}}
===Definition===
The angle between two normal plane vectors.

<center><math>\xi = arccos \left( \bold n_A . \bold n_B \right)</math></center>

The planes are defined as the best fit among atoms in each atom group. The fit is mass weighted.
<center><math>\psi(\bold n_A^') = \sum_{i=1}^{group_A}{m_i[\bold n_A^' .( \bold x_i - \bold A_{com})]^2} \rightarrow min!</math></center>
<center><math>\psi(\bold n_B^') = \sum_{i=1}^{group_B}{m_i[\bold n_B^' .( \bold x_i - \bold B_{com})]^2} \rightarrow min!</math></center>

The orientation of the plane normal vectors is controled by two helper vectors '''x'''dir and '''y'''dir:
<center><math>\bold n_A = sign( \bold n_A^' . (\bold x_{dir,a} \times \bold y_{dir,a}) ) \bold n_A^'</math></center>
<center><math>\bold n_B = sign( \bold n_B^' . (\bold x_{dir,b} \times \bold y_{dir,b}) ) \bold n_B^'</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''PANG'''
{|
| 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 plane '''A'''
|- style="vertical-align: top;"
| '''x_direction_a'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate x-direction vector. The vector origin is in '''A'''com. The atom must be member of the group '''A'''.
|- style="vertical-align: top;"
| '''y_direction_a'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate y-direction vector. The vector origin is in '''A'''com. The atom must be member of the group '''A'''.
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the plane '''B'''
|- style="vertical-align: top;"
| '''x_direction_b'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate x-direction vector. The vector origin is in '''B'''com. The atom must be member of the group '''B'''.
|- style="vertical-align: top;"
| '''y_direction_b'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate y-direction vector. The vector origin is in '''B'''com. The atom must be member of the group '''B'''.
|-
|}
''Keys in bold are mandatory.''

CV:DIH

2015-06-09T13:28:13Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:DIH ---- {{CVS}} ===Definition=== The dihedral angle among four points. Each point is calcu..."

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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:DIH]]
----
{{CVS}}
===Definition===
The dihedral angle among four points. Each point is calculated as the center of mass of groups of atoms.
<center><math>\xi = sign(\bold n_2 . ( \bold A_{com} - \bold B_{com} ) )*arccos \left(\frac{ \bold n_1 . \bold n_2 }{|\bold n_1| . | \bold n_2 |} \right)</math></center>
where normal vectors are defined as
<center><math>\bold n_1 = ( \bold A_{com} - \bold B_{com} ) \times ( \bold C_{com} - \bold B_{com} )</math></center>
<center><math>\bold n_2 = ( \bold C_{com} - \bold B_{com} ) \times ( \bold C_{com} - \bold D_{com} )</math></center>

'''PBC note:''' The minimum-image convention is apllied to vectors |AB|, |CB|, 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.

===Specification===
Section name: '''DIH'''
{|
| 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.''

CV:AXANG

2015-06-09T13:23:05Z

Tbouchal: Created page with "__NOEDITSECTION__ Navigation: Documentation / Collective Variables / CV:AXANG ---- {{CVS}} ===Definition=== The angle between two axes of two principal moments of..."

__NOEDITSECTION__
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:AXANG]]
----
{{CVS}}
===Definition===
The angle between two axes of two principal moments of the gyration tensor.

<center><math>\xi = arccos \left( \bold n_A . \bold n_B \right)</math></center>

The mass weighted gyration tensor '''S''' is defined as

<center><math>S_{mn} \ = \frac {\sum_{i=1}^{N} m_i (x_{m}^{(i)} - x_{m}^{(\bold A)}) (x_{n}^{(i)} - x_{n}^{(\bold A)})}{\sum_{i=1}^{N} m_i} </math></center>

The eigenvalues of the tensor are <math>\lambda_{x}^2 \leq \lambda_{y}^2 \leq \lambda_{z}^2</math>:
<center><math>
\bold S = \begin{bmatrix}
\lambda_{x}^{2} & 0 & 0 \\
0 & \lambda_{y}^{2} & 0 \\
0 & 0 & \lambda_{z}^{2}
\end{bmatrix}
</math></center>

'''PBC note:''' The minimum-image convention is not used.

===Specification===
Section name: '''AXANG'''
{|
| 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 axis '''A'''
|- style="vertical-align: top;"
| '''head_a'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate vector in the direction of principal moment. The vector origin is in '''A'''com. The atom must be member of the group '''A'''.
|-
| '''direction_a'''
| x, y, z
|
| select corresponding principal moment vector
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying the axis '''B'''
|- style="vertical-align: top;"
| '''head_b'''
| [[Mask format|mask]]
|
| single atom specifying the end of approximate vector in the direction of principal moment. The vector origin is in '''B'''com. The atom must be member of the group '''B'''.
|-
| '''direction_b'''
| x, y, z
|
| select corresponding principal moment vector
|}
''Keys in bold are mandatory.''

CV:ANG

2015-06-09T13:22:30Z

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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:ANG]]
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{{CVS}}
===Definition===
The angle among three points. Each point is calculated as the center of mass of groups of atoms.
<center><math>\xi = arccos \left(\frac{( \bold A_{com} - \bold B_{com} ) . ( \bold C_{com} - \bold B_{com} )}{| \bold A_{com} - \bold B_{com} | | \bold C_{com} - \bold B_{com} |} \right)</math></center>

'''PBC note:''' The minimum-image convention is apllied to distances |AB| and |CB| 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.

===Specification===
Section name: '''ANG'''
{|
| 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 point '''A'''
|-
| '''group_b'''
| [[Mask format|mask]]
|
| atoms specifying point '''B'''
|-
| '''group_c'''
| [[Mask format|mask]]
|
| atoms specifying point '''C'''
|}
''Keys in bold are mandatory.''