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

[Justin A. Lemkul]

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

-- 
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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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