[gmx-users] Ngmx

[karamyog singh]

i think since i do not have cell as of now.. i.e with 0.5 0.5 0.5 cell size
and also with 1.0 1.0 1.0 cell size , gromacs is not able to generate pbc.

On 5/11/06, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
>
> 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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