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
off.
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...
Chris.
-- 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.
Daniel
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.
Cheers,
Tsjerk
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