[gmx-users] Ngmx

karamyog singh karamyog.singh at gmail.com
Thu May 11 15:36:27 CEST 2006

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?


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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