[gmx-users] Ngmx

[Tsjerk Wassenaar]

Karam,

If you think you know why, please share your thoughts.. that can help us
provide an answer.

Still, gromacs supports all periodic boundary conditions, except for real
exotic stuff like spherical (and I can think of a few others). But any
crystal packing can be handled. Maybe the easiest for you is to build a
single bcc unit cell, with the correct lattice vectors as the box
definition. Then run genbox to copy that a certain number of times. Also
read the gromacs manual to understand the definition of the box (last line
of the .gro file) if you haven't done so.

Tsjerk

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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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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