On 1/12/2011 10:24 AM, mu xiaojia wrote:
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?
Observe the box created by -d 1.0 and then start again with editconf
-box and choose dimensions you want.
Mark
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