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

[Tsjerk Wassenaar]

Hi Rajan,

The center of the system is the center of mass, not the center of the
bounding box.

Cheers,

Tsjerk

On Sat, Mar 14, 2015 at 8:41 PM, Rajan Kumar <kumarrajan513 at gmail.com>
wrote:

> 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
> --
> Gromacs Users mailing list
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-- 
Tsjerk A. Wassenaar, Ph.D.