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

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 21 16:44:05 CEST 2008

Michael Hirtz wrote:
> 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.

Right, so search the manual for *topology* and you will find the information 
about the appropriate format.  If you want a GROMOS-compatible topology, PRODRG2 
might be of use, otherwise you'll have to make the topology by hand.

> 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]).

Again, search the manual for these relevant keywords, as they are explained in 
Chapter 5.

> 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...

You can add position restraints on whichever atom(s) you choose, provided that 
such restraints accurately suit your needs.  I don't know what you mean by 
"build up the substrate," however...


> Any comments/suggestions , anyone?
> Thanks,
>    Michael
>> 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.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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