Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes.
Ran. Léon Salgado wrote: > Dear gmx users > > I did some simulations of multimers (peptides) in rhombic dodecahedron > boxes. In the initial configuration of the system, the peptides are > close of each other in the center of the box. > > My aim to see if the peptides do aggregate during the trajectory or if > they tend to stay apart. A rough estimate can be taken from the > gyration radius for all the peptides together. > > Already did a trjconv -pbc nojump pre-treatment on the trajectory, > before calculating the Rgyr. The gyration.xvg plots sometimes do show > abrupt jumps, and this is surely due to boundary effects, if I > correctly understood the PBC idea. If a peptide approaches the > boundary, it appears on the opposite side, thus rgyr will show a false > sudden increase. In fact, the peptide could be closer to the rest of > the other peptide molecule(s). > > Thus my question is: > how to deal with peptide clusters that span over the periodic boundaries? > > A similar question was done by Singh: > http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html > > and it was suggested by Chris Neale to pre-process the trajectory > (see > http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) > with: > > trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster > grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr > trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump > > but I'm getting infinite loops on the -pbc cluster treatment, same as > reported by Chris > (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). > > Best, > Léon > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
