[gmx-users] Clustsize

Sohaib. Mohammed sohaibmohammed10 at gmail.com
Tue Apr 18 19:47:11 CEST 2017

Dear all,

I performed NPT simulation for 480 united atom of n-Octane for 60 ns with
quenching from 250 to 170 K at t = 0. I expect to see different cluster
sized and I noticed so by VMD. I want to calculate the maximum cluster size
as a function of time. I used the following command :
 gmx clustsize -f npt_noPBC1.xtc -s npt.tpr -o csize1.xpm -cut 0.35 -mol
The result is as following
Total number of atoms in clusters =  477
cmid: 1, cmax: 472, max_size: 480
cmid: 3, cmax: 480, max_size: 480
I get the max cluster is equal the total number of molecules from the
beginning of the run and stay constant along with the time.
I think this is not correct because it can be easily noticed that there are
different clusters in the VMD and the max. cluster is about 50-60 molecule.

Appreciate any suggestions, ideas and comments.

Thank you

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