G_cluster for size group

User discussions
1

GROMACS version:2020.4
After finishing my simulation i used g_cluster command to find the size group but among these group , i got one group with only one frame so should i discard this from my analysis ?

2

Hi,
could you re-formulate your question?
gmx cluster is a tool to cluster structures using several different methods, while gmx clustsize computes the size distributions of molecular/atomic clusters in the gas phase.
Thank you
Alessandra

3

Thanks for replying , sorry i mean gmx cluster

4

Hi,
I try to see if I understood, you have run gmx cluster after your simulation to see possible cluster among your structures, and you got as output a log file where only one cluster has been identified.

You can look at the methods you have used and the criteria you have used and tune them to be able to identify possible clusters.

see more gmx cluster — GROMACS 2020.5 documentation

Best regards
Alessandra

5

appreciating your reply … Thanks for helping …
I got 12 group of cluster but one of them has only one structure So if i want to make further analysis should i discard this group ?

6

It depends which type of analysis do you want to perform. Note that the population of the cluster depends on the methods you have to select for clustering and on the criteria (e.i cutoff) you have provide in gmx cluster (gmx cluster — GROMACS 2020.5 documentation).
Best regards
Alessandra