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

[Rajan Kumar]

Hi Tsjerk,

Please see the box here
https://www.dropbox.com/s/cu70fw2dmwaxl1x/Editconf.png?dl=0.

On Sat, Mar 14, 2015 at 1:38 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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-- 
Rajan Kumar
Indian Institute of Technology, Guwahati