[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
>> 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
> 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?
>> On Tue, Jul 15, 2008 at 9:37 AM, Michael Hirtz <hirtz at uni-muenster.de
>>> 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,
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at http://www.gromacs.org/search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> Diego Enry B. Gomes
>> Laborat�rio de Modelagem e Dinamica Molecular
>> Universidade Federal do Rio de Janeiro - Brasil.
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users