Shortcut: AROUND
| Module | volumes |
|---|---|
| Description | Usage |
| This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. |   |
| output value | type |
| sum of values of input CVs in regin of interest | scalar |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action’s label followed by a dot and the name of the value required from the list below.
| Name | Type | Keyword | Description |
|---|---|---|---|
| lessthan | scalar | LESS_THAN | the number of cvs in the region of interest that are less than a certain threshold |
| morethan | scalar | MORE_THAN | the number of cvs in the region of interest that are more than a certain threshold |
| between | scalar | BETWEEN | the number of cvs in the region of interest that are within a certain range |
| sum | scalar | SUM | the sum of all the colvars weighted by the function that determines if we are in the region |
| mean | scalar | MEAN | the average values of the colvar in the region of interest |
Input
The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ATOMS | atoms | the group of atoms that you would like to investigate |
| ORIGIN | atoms | the atom whose vicinity we are interested in examining |
| ATOM | atoms | an alternative to ORIGIN |
Further details and examples
Text from manual goes here
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ATOMS | input | none | the group of atoms that you would like to investigate |
| ORIGIN | input | none | the atom whose vicinity we are interested in examining |
| ATOM | input | none | an alternative to ORIGIN |
| SIGMA | compulsory | none | the width of the function to be used for kernel density estimation |
| KERNEL | compulsory | gaussian | the type of kernel function to be used |
| XLOWER | compulsory | 0.0 | the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box) |
| XUPPER | compulsory | 0.0 | the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box) |
| YLOWER | compulsory | 0.0 | the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box) |
| YUPPER | compulsory | 0.0 | the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box) |
| ZLOWER | compulsory | 0.0 | the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box) |
| ZUPPER | compulsory | 0.0 | the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box) |
| SERIAL | optional | false | do the calculation in serial |
| OUTSIDE | optional | false | calculate quantities for colvars that are on atoms outside the region of interest |
| DATA | optional | not used | the label of an action that calculates multicolvars |
| LESS_THAN | optional | not used | calcualte the number of colvars that are inside the region of interest and that are less than a certain threshold |
| MORE_THAN | optional | not used | calcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold |
| BETWEEN | optional | not used | calculate the number of colvars that are inside the region of interest and that have a CV value that is between a particular set of bounds |
| SUM | optional | false | calculate the sum of all the quantities |
| MEAN | optional | false | calculate the average value of the colvar inside the region of interest |