Gmx Clustsize Error

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hi everyone! I am trying to compute the size distribution of a protein cluster using the following command -
gmx clustsize -f *xtc -s *tpr -n *ndx -cut 2.5 -o clust.xpm -nc nclust.xvg -mc mclust.xvg -tu ns
However, I keep getting the same error as shown.
image

Why does it show that all atoms are part of a single cluster? Visually I can see there are two clusters. I have tried with different cut offs too. Are there any other tools to get the size distributions of a protein cluster?

Any help is appreciated. Thank you.

2

Can anyone help me with how to properly choose the cut in gmx clustsize?

3

Hello, have you been able to find a solution? I am having a similar problem and couldn’t find any information on the internet. I have a liquid system which I’m sure it clusters from the rdf analysis but it keeps giving that fatal error when I run gmx clustsize command.