[gmx-users] Placing system at the centre of the box.

[Tsjerk Wassenaar]

Hi Rajan,

Do you see the box?
>From your output it is easily seen that the new center equals
0.5*boxvectors.

Cheers,

Tsjerk
On Mar 14, 2015 5:47 AM, "Rajan Kumar" <kumarrajan513 at gmail.com> wrote:

> Hi all,
>
> I am trying to study wetting of water on Graphene oxide(GO). My
> structure has functional group in form of epoxide group
> on one side of the Graphene sheet. Also I have added water
> molecules in form of spherical droplet on the same side of the sheet.
>
> I used the following commands to generate .gro.
>
> editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c
>
> ---------------------------------
>
> Read 260 atoms
> No velocities found
>     system size :  1.845  1.562  1.523 (nm)
>     center      :  0.985  0.828  0.380 (nm)
>     box vectors :  0.000  0.000  0.000 (nm)
>     box angles  :   0.00   0.00   0.00 (degrees)
>     box volume  :   0.00               (nm^3)
>     shift       :  0.515  0.672  1.120 (nm)
> new center      :  1.500  1.500  1.500 (nm)
> new box vectors :  3.000  3.000  3.000 (nm)
> new box angles  :  90.00  90.00  90.00 (degrees)
> new box volume  :  27.00               (nm^3)
>
>
> ----------------------------------------------------------------------------
>
> My question is, what is this* center* and how is it calculated by editconf?
> When I see conf.gro in VMD, I don't actually see my system at the geometric
> center of the box.
>
>
> ​
>
> --
> Rajan Kumar
> Indian Institute of Technology, Guwahati
>
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