[gmx-users] Ngmx

karamyog singh karamyog.singh at gmail.com
Thu May 11 16:05:07 CEST 2006

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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