[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Daniel Parton daniel.parton at bioch.ox.ac.uk
Tue Dec 1 14:55:43 CET 2009


I've tried using trjconv -pbc nojump with a .tpr created from the first 
frame of the trajectory (clustered so the vesicle should be whole). The 
output trajectory starts with a complete vesicle, but small numbers of 
lipid particles progressively move to places outside of the box. By the 
end of the trajectory there appear to be 8 groups of particles outside 
the box, which have the same overall spherical shape as the vesicle, but 
are comprised of only a few hundred particles. I have uploaded some 
pictures here:

traj-start is the first frame of the unprocessed trajectory:

traj-end is the last frame of the unprocessed trajectory:

nojump-start is the first frame of the trajectory following trjconv -pbc 
nojump, as described above. The vesicle starts whole:

nojump-end is the last frame of the trajectory following trjconv -pbc 
nojump. Note that some particles have moved to being outside the box, 
seeming to take up space resembling 8 copies of the vesicle system.

0ns-cluster is the first frame of the trajectory, clustered using 
trjconv -pbc cluster. The pbc option may have gone a bit wrong? 
Particles which should be very close to the box boundary seem to have 
been moved to other places in or outside the box. Other parts which lie 
some way inside or outside the box appear (correctly) as part of the 

So I am wondering the problem lies with the 0ns-cluster system. As some 
particles are not part of the vesicle in this representation, this could 
explain why some particles are not being counted as part of the vesicle 
by trjconv -pbc nojump. Does this seem likely, and has anyone seen 
similar behaviour to that seen in 0ns-cluster, where trjconv -pbc 
cluster has been used with a rhombic dodecahedron box?

Many thanks for all of your help so far,


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