Shortcut: OUTPUT_CLUSTER

Module	clusters
Description	Usage
Output the indices of the atoms in one of the clusters identified by a clustering object

Details and examples

Output the indices of the atoms in one of the clusters identified by a clustering object

This action provides one way of getting output from a DFSCLUSTERING calculation. The output in question here is a gromacs ndx file that contains a list of the atom indices that form part of one of the clusters that was identified using DFSCLUSTERING

The input shown below constructs a CONTACT_MATRIX that describes the connectivity between the atoms. The DFS algorithm is then used to find the connected components in this matrix. The indices of the atoms in the largest connected component in each frame of the trajectory are then output to a ndx file.

Click on the labels of the actions for more information on what each action computes

matThe CONTACT_MATRIX action with label mat calculates the following quantities:
 Quantity   
 Type   
 Description  
mat
matrix
a matrix containing the weights for the bonds between each pair of atoms: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ATOMSYou should use GROUP instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=1-1996 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=0.34 D_MAX=0.38}
dfsThe DFSCLUSTERING action with label dfs calculates the following quantities:
 Quantity   
 Type   
 Description  
dfs
vector
vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of: DFSCLUSTERINGFind the connected components of the matrix using the depth first search clustering algorithm. More details ARGthe input matrix=mat
OUTPUT_CLUSTEROutput the indices of the atoms in one of the clusters identified by a clustering object More details ATOMSthe atoms for which clustering were performed=1-1996 CLUSTERSthe action that performed the clustering=dfs CLUSTER which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on=1 FILEthe name of the file on which to output the details of the cluster=dfs.ndx STRIDE the frequency with which you would like to output the atoms in the cluster=1

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ATOMS	compulsory	none	the atoms for which clustering were performed
CLUSTERS	compulsory	none	the action that performed the clustering
CLUSTER	compulsory	1	which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on
STRIDE	compulsory	1	the frequency with which you would like to output the atoms in the cluster
FILE	compulsory	none	the name of the file on which to output the details of the cluster

References

More information about how this action can be used is available in the following articles:

• G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)