Gmx clustsize -hc flag

User discussions
1

Dear user,

I am working with the command gmx clustsize to understand how many molecules are not in the clusters, since I see them form VMD visualization.

I am using these commands:

gmx clustsize -f cluster.xtc -s cluster.tpr -n index.ndx -cut 0.45 -nskip 10 -xvg none -nc cluster.xvg -hc histo.xvg -mc max.xvg

but I didn’t understand what the -hc output gives. Does it give a probability?

Thanks.

Giuseppe

2

Hi,
the option -hc provides the distribution of the cluster size. Note that you need to provide the option -mol to have information on molecular cluster.
Regards
Alessandra