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
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.fried...@lnu.se
http://lnu.se/ccbg
From: Stefano [boro...@unitus.it]
Sent: 26 July 2011 15:49
To: Ran Friedman
Subject:
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
VMD).
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
+39-0761-357193
Fax +39 0761-357179
e-mail: boro...@unitus.it
---
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