GROMACS version: 2018
GROMACS modification: Yes/No
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I would like to use gmx clustsize to monitor time evolution of number of clusters formed by a molecule. My question is does it take all atoms into consideration while performing calculations? To me more specific, if I use:
gmx clustsize -f *.xtc -s *.tpr -mol -cut 0.45
and select my ligand molecule (which forms aggregate with time)
In that case, I just want to confirm if I understand correctly, two ligand molecules are defined to be in cluster if the largest distance between them (any atom of ligand molecule) is 0.45 nm. Herein, all atoms of ligand molecules are considered while performing calculations.
Please correct me if I am missing anything.
Hi,
gmx clustsize computes the size distributions of molecular/atomic clusters in the gas phase. Is this what you want?
Did you check gmx cluster (gmx cluster — GROMACS 2021.2 documentation)?
Best regards
Alessandra