[gmx-users] Regargding simulation of periodic silica surface

Sathish Kumar sathishk238 at gmail.com
Fri Sep 12 09:15:48 CEST 2014

         I am trying to run simulation of silica surface with lipid
membrane, but i am not able to create periodic structure of silica surface.
I constructed one surface for that i have not mention periodic molecule in
the mdp file, and i fix the box such that the distance from x,y and z is 2
nm and then i kept the lipid membrane above the surface. while running nvt
for this structure, its creating some pdb files like step_0.pdb and it is
getting stop. Can any please suggest me how to run this type of simulation
and if any body have structure of silica surface and its topology please
give to me. It would be helpful to my work.


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