[gmx-users] Regargding simulation of periodic silica surface

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Fri Sep 12 12:17:51 CEST 2014

On 12.09.2014 09:15, Sathish Kumar wrote:
> 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.

It's not clear what you did here. Did you prepare a block of
(not charge-neutral) SiO2 in the center of your simulation
box, and treat it like a block of charged single atoms
in a crystalline configuration? Then, did you hydroxylate
and/or oxidize dangling Si and O bonds on the block surface?

> while running nvt  for this structure,
> its creating some pdb files like step_0.pdb and it is
> getting stop.

What type of interaction potentials did you use for SiO2 and
how is the charge treated? In your md.log file produced during
your trial, there are blocks of values like

            Coulomb    Potential    Kinetic En. Temp. ...

with corresponding values. Can you post one of these blocks
here or make the md.log available elsewhere?

> Can any please suggest me how to run this type of simulation
> give to me. It would be helpful to my work.

You'd construct a SiO2 (crystobalite) block using vmd's
'inorganic builder' (say: 10 x 10 x 2 elementary cells),
translate (in vmd) these coordinates to values above/equal
zero and write the structure as .gro format. This should give
you a x/y-periodic block. Then, you enlarge z (with
gromacs tools) and post-process the two emerging "surfaces"
of your formerly periodic block. Post-processing involves
saturation of dangling bonds by hydroxylation and/or
creation of O-Si-O-bridges.



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