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.
Mark
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