[gmx-users] Ngmx

[Tsjerk Wassenaar]

Hi Karamyog,

First build the crystal consisting of the number of atoms you want to
include, using the crystal lattice vectors. Than build your unit cell as to
contain these. Again use the crystal lattice vectors, but scale them for the
size of your crystal unit cell. So, if your crystal is 10x10x10 atoms, your
unit cell is 10*v1, 10*v2, 10*v3, where v1, v2 and v3 are the lattice
vectors between the atoms.

Cheers,

Tsjerk

On 5/11/06, karamyog singh <karamyog.singh at gmail.com> 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.
>
> 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?
>
> -
> karamyog
>
> On 5/11/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> >
> > karamyog singh wrote:
> > > Respected gentlemen, I have written another code for simulating atomic
> > > oxygen. the code is running fine. however when i view my run using
> > ngmx,
> > > the entire box doesn't get filled up.It just shows one plane of atoms.
> > I
> > > have a box of 27 atoms but ngmx shows only 9. Can any1 tell me why and
> > > the solution to this problem.
> >
> > >  27MY   OX   27  0.000000   0.250000  0.500000 ; 0.000 0.000 0.000
> > > 0.5 0.5 0.5
> >
> > Your box is of size 0.5x0.5x0.5, so atom 27 overlays exactly with some
> > other atom at 0,0.25,0... evidently you are doing this with all of your
> > 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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