Clarification of the compute cluster/atom command

To whom it may concern,

I would like some clarification of the compute cluster/atom command. I have chains with 3 ‘sticker’ beads on each end. I want to perform a cluster analysis during a simultion. I want the number and size of the clusters. Using the compute cluster/atom command with a cutoff of 1.2, I output a trajectory file with my data. However, I notice that there are multiple single beads in the cluster analysis when in reality, there shouldn’t be any. The smallest cluster size should be 3. I am wondering if this command only takes into account the LJ non-bonded interactions? And if so, would the 1st and 3rd ‘sticker’ bead in each chain be counted in the same cluster? I am just trying to understand the output and any help would be greatly appreciated.
Morgan Popa

The compute does not take into consideration any pair styles. It only needs atom position, not forces. You might need to play around with the cutoff to get what you want.


Here’s another thing to consider. The compute cluster/atom

doc page should have the same warning the compute rdf doc

page does (I just added it to the former).

IMPORTANT NOTE: If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included in the RDF. This does not apply when using long-range coulomb (coul/long, coul/msm, coul/wolf or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the rerun command to compute the RDF for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.

It sounds like you have bonds in your system, so this is relevant

to interpreting the cluster sizes.


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