[gmx-users] Re: Simulation of silicon oxide surfaces

Michael Hirtz hirtz at uni-muenster.de
Mon Jul 21 16:03:08 CEST 2008

Hi Diego, hello other gmx-users participants,

> Hi Michael, look for the bionano tutorial at VMD site. It will
> instruct you how to use TCL to build your SiO surface from an "unit
> cell".
> In a near future they will release the "inorganic builder plugin" that
> will make things a LOT easier.

Thanks for your reply! I haven't seen the tutorial before, so that gave me
already some good background for the creation of substrates. But my main
problem was not so much to get the structure (as pdb or similar) at all but to
translate it to a GROMACS topography (like they used scripts for to generate a
.psf in the bionano tutorial). I had found the inorganic builder plugin before
(you can already download and install it to vmd), but still only end up with a
.pdb that of course cannot be translated by pdb2gmx because it doesn't
recognize the residues.

When I look at the .psf for the SiN membrane of the tutorial, it seems that
the whole substrate is introduced as one molecule. Of course I could build
something similar in a GROMACS topography and define all necessary bonds, but
what atomtypes should be used and what for the other parameters ([pairs],
[angles] and [dihedrals]).

Or would it be feasible to use single position restraint Si and O atoms (or
maybe better SiO2 molecules) to build up the substrate? Since I only need the
surface and it doesn't matter whether it's crystaline or amorphous I guess
that would be also ok...

Any comments/suggestions , anyone?


> On Tue, Jul 15, 2008 at 9:37 AM, Michael Hirtz <hirtz at uni-muenster.de
>> wrote:
>> Hello,

>> I want to set up a silicon oxide surface with varying -OH surface group
>> for my simulation. Does anybody know a tool that could do that or maybe
>> even has a topology I could start on and alter manually?

>> Thanks for any sugesstions,
>>    Michael
>> --
>> http://www.defux.de
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> --
> Diego Enry B. Gomes
> Laborat&#65533;rio de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.

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