[gmx-users] control Distance between the solute and the box for 3 directions seperately

[mu xiaojia]

Dear gmx-users,

I want to make a long nano-fiber composed of many non-covalently bonded
proteins, it elongates along the Z axial direction.

in editconf, we can define the "Distance between the solute and the box",
but it works for x,y and z directions at the same time.

e.g. my command
editconf -f protein.gro -o protein_box.gro -c -d 1.0 -bt cubic,    then the
out come would be a box with  of at least 1.0 nm "between any two periodic
images of a protein".

What should I do if I want to set the distance for z axis smaller than x
and y? which means, let the molecules along Z "see" each other within 2nm?


Thanks!

Xiaojia
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