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?
Set the box size manually with editconf -box. Beware that if you make a
rectangular box around your nanofiber, if it rotates, you may violate the
minimum image convention.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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