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

[Rajan Kumar]

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.


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-- 
Rajan Kumar
Indian Institute of Technology, Guwahati