[gmx-users] Ngmx

[karamyog singh]

the problem continues even if i rescale my box to 1.0 1.0 1.0 :(

On 5/11/06, karamyog singh <karamyog.singh at gmail.com> wrote:
>
> hmm.. i know about the no. of atoms in bcc. please tell me what to do if i
> want more than 1 unit cell?
> gromacs is not supporting periodic boundary conditions for my cell and i
> think i know y.
> On 5/11/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> > karamyog singh wrote:
> > > Thnx Mark. I stil have a doubt. If want to simulate a crystal
> > > structure,then how should i go about it? wht changes should be made in
> > > the above file? even if i replace the 27th atom with 0.5 0.25 0.5,
> > then
> > > too it will overlay some other atom.
> >
> > 0.5 == 0 if the size is 0.5. If you've got the atom spacing right for 27
> > atoms in this configuration, then increase your box size to make the
> > periodic images go in the right spots. At the moment you are overlaying
> > atoms.
> >
> > > I understand wht the fault with my conf.gro file is, but if I have to
> > > simulate a bcc lattice then wht should the .gro file look like?
> >
> > IIRC, a bcc lattice has two atoms per unit cell e.g . the central one
> > and
> > eight eighths of an atom at each of the cube vertices. Thus I have no
> > idea what you're trying to do with 27 atoms.
> >
> > Mark
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>
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