[gmx-users] Peptide aggregation

Léon Salgado leon.salgado at gmail.com
Fri Sep 19 16:43:26 CEST 2008

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:

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 


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