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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Nov 30 23:38:33 CET 2009

Hi Daniel,

I think you still need to read and attempt what has already been  
suggested. To be more explicit:

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

from: http://lists.gromacs.org/pipermail/gmx-users/2007-January/025388.html

And if the first -pbc cluster doesn't work, then try:

trjconv -f a.xtc -o a_cluster.gro -b 0.001 -e 1.001 -pbc cluster

or similar.


--- original message ---


Thanks for the suggestion to use trjconv -pbc nojump. Unfortunately, it
has not worked, as the vesicle is still not whole in the trajectory. I
have tried subsequently centering the trajectory, and representing the
system with -ur compact, but still it does not work. I am wondering if
the problem lies with the initial frame. I don't understand very well
the geometrical theories for how it is possible to represent a rhombic
dodecahedron as a triclinic box, so I'm relying only on what I see when
viewing the system with VMD. But looking at the first frame, it appears
to be impossible for the vesicle to be whole in the triclinic box. After
converting with trjconv -ur compact, the system appears as expected -
the vesicle is whole and centered, with a shell of water around it,
extending to the edges of the rhombic dodecahedron box.

So my feeling is that although the vesicle appears to be whole when
viewed with the compact representation, it is impossible to make the
vesicle whole in the triclinic representation, as certain dimensions of
the box are too small. Just as further explanation, I think that if the
box:vesicle size ratio was larger, then it should be possible to fit the
whole vesicle in the triclinic box. Thus trjconv -pbc nojump does not
help, as the vesicle is not whole in the first (or any) frame. Does this
make sense, and would it seem likely to be the problem? And if so, could
there be a way around this problem?



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