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

[Mark Abraham]

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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