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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Dec 1 19:25:39 CET 2009

There is no problem with the rhombic dodecahedron in and of itself.  
Note that editconf -d does not actually yield the -d that you ask it  
to and that it errs on different sides of your request for different  
box types. To prove this to yourself, run your starting structure  
through editconf -d with a variety of -bt options and then run  
g_mindist -pi on the output .gro. You will see the variation straight  

Stick with the rhombic dodecahedron... just use a larger one. Use  
g_mindist -pi to get an idea of the actual separation that you have  
obtained, and keep in mind that the surface of the vesicle is rugged  
and fluctuating, therefore you will need to have enough of a water  
layer to prevent spontaneous fluctuation-based merger events.

On the up-side, you seem to have a system that can shed light on the  
process of vesicle merger...


-- original message --

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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