[gmx-users] Regargding simulation of periodic silica surface

[Mirco Wahab]

On 12.09.2014 16:16, Sathish Kumar wrote:
> So in SiO2 structure atoms are getting merged, is that the reason for the
> error in simulation?

Aside from the y-PBC overlap, please look closer into
your coordinates:

...
...
1882MAK     Si 1710   6.303   0.003   4.160
...
...
...
4480SOB     BO 6359   6.303   0.003   4.160
...
...

Where did you get these coordinates from? They seem
to need another cleanup and preprocessing step before
simulation.

Regards

M.