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

Daniel Parton daniel.parton at bioch.ox.ac.uk
Tue Dec 1 16:46:23 CET 2009

Ok, I guess in future I will have to make sure the box is big enough to contain the entire vesicle in the triclinic representation. It's kind of a shame though, as the main reason for using the rhombic dodecahedron box was to minimize the amount of bulk solvent required.

Thanks for your help though.


Hi Daniel,

The problem is likely that your vesicle is interacting with itself
over the periodic boundaries. There are regions where there is no
solvent inbetween. That means that lipids can go over from one image
to the other by diffusion, which will not be compensated by using -pbc
nojump. You seem to be out of luck there.
The solution to solve this problem would be to rebuild the vesicle by
minimizing the sum of squared deviations from the center using shifts
over the lattice. But that is not implemented.



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