[gmx-users] Simulating crystalls

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 25 02:44:45 CEST 2006

karamyog singh wrote:
> I am trying to simulate a crystal too. I have a box size of .65 nm and 
> there are 8 bcc crystals in the system. Lattice parameter = 0.287 nm.
> I get a segmentation fault after mdrun -v. Is an atom with co-ordinates 
> 0.574 0.000 0.000 equivalent to 0.287 0.000 0.000 in such a system?

Cubic PBC with side length l means that (x,y,z) is equivalent to 
(x+al,y+bl,z+cl) for any integers a,b and c.

> What 
> I am trying to ask is, does GROMACS consider these as 2 different atoms 
> placed at the respective positions or do the 2 atoms overlap?

No. GROMACS takes every atom you give in the .top file and uses it - 
there is no attempt to check for symmetry simplifications such as 
quantum chemistry codes do.

> What could be the reason for the segmentation fault? Is it because the 
> atoms are too close to each other?

You're on your own here unless you can provide more information.


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