[gmx-users] Peptide aggregation

Ran Friedman r.friedman at bioc.uzh.ch
Fri Sep 19 17:29:59 CEST 2008

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.


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
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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: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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