[gmx-users] RE: g_clustsize

Ran Friedman ran.friedman at lnu.se
Thu Jul 28 16:45:44 CEST 2011

Dear Stefano,

I forward your question to the gromacs-users mailing list. Please send further inquiries there - there may be people more qualified than me to reply (unless you refer to my modified version or to one of my papers)

I'm not sure if the .xpm files give the information you're interested at but using g_clustsize -av and -hc is useful to get the average size and distribution. You can further use -mcn and extract the index group of the largest cluster. By a combination of scripting and other Gromacs tools you can get more info on the largest cluster per frame if you need it.

g_clustsize doesn't give you the radius of gyration of the cluster. My modified version does, but only for the largest cluster - not for all as you need I guess.

Good luck,

Ran Friedman
Biträdande Lektor (Assistant Professor)

Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden

Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.friedman at lnu.se

From: Stefano [borocci at unitus.it]
Sent: 26 July 2011 15:49
To: Ran Friedman

Dear Prof Friedman
I am Stefano Borocci, a GROMACS user.
I am currently studying, through molecular dynamics simulations, the
self-assembly of Gemini surfactants.
I have some problems to use the g_clustsize of GROMACS and  I don't
understand the results obtained with this tool.

I have analyzed the xtc file of my trajectory

g_clustsize -f trj.xtc -s top.tpr -mol (and without) -cut 0.35

and the cluster size and cluster distributions predicted by g_clustsize
does not match with what I see by a visual analysis of trajectory (using
I also tried to remove the periodic boundary (-pbc mol) without result.
I have two questions:
How to calculate the cluster (micelle) size and cluster distribution of
my sistem?
How to calculate the radius of gyration of the aggregates if in my box
there are more clusters (3 or 4)?

I would be very grateful if you could help me
Thanks in advance.

Best regards

                                                                          Stefano Borocci

Dr Stefano Borocci
Laboratorio di Chimica e Chimica Computazionale
Dipartimento per la Innovazione nei Sistemi Biologici,
Agroalimentari e Forestali (DIBAF)
Università degli Studi della Tuscia
Largo dell'Università, snc 01100 Viterbo
Tel. +39-0761-357127
Fax  +39 0761-357179
e-mail: borocci at unitus.it

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