[gmx-users] Simulating crystalls
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.
> 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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