Action: WHOLEMOLECULES
| Module | generic |
|---|---|
| Description | Usage |
| This action is used to rebuild molecules that can become split by the periodic boundary conditions. |   |
| This action outputs data to a file. You can read more about how PLUMED manages output files here |
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 |
|---|---|---|
| ENTITY | atoms | the atoms that make up a molecule that you wish to align |
| RESIDUES | atoms | this command specifies that the backbone atoms in a set of residues all must be aligned |
Further details and examples
Text from manual goes here
References
More information about how this action can be used is available in the following articles:
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ENTITY | input | none | the atoms that make up a molecule that you wish to align |
| RESIDUES | input | none | this command specifies that the backbone atoms in a set of residues all must be aligned |
| STRIDE | compulsory | 1 | the frequency with which molecules are reassembled |
| MOLTYPE | optional | not used | the type of molecule that is under study |
| EMST | optional | false | Define atoms sequence in entities using an Euclidean minimum spanning tree |
| ADDREFERENCE | optional | false | Define the reference position of the first atom of each entity using a PDB file |