[gmx-users] Ngmx

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 11 15:54:54 CEST 2006

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 

> 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.


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