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 [email protected] http://lnu.se/ccbg ------------------------------------------------ ________________________________________ From: Stefano [[email protected]] 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: [email protected] ----------------------------------------------- -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
