[gmx-users] Peptide aggregation

Léon Salgado leon.salgado at gmail.com
Fri Sep 19 18:13:02 CEST 2008

Dear Dr. Ran Friedman

Would you please be so kind to send me your version, to calculate then 
the rgyr "of the largest aggregate".
The box was built with a layer of 1.2 nm around the solute (editconf -d 


Ran Friedman wrote:
> 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
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