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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 22 21:40:27 CEST 2008

Michael Hirtz wrote:
> Hi Justin,
> Thank you for answering my mail. I'm new to GROMACS, but of course I checked
> the manual before posting here... :) I succeeded in generating some other
> topologies of smaller molecules, but still my problems in generating a SiOx
> substrate persist.
>>> 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.
> I used PRODRG before to generate topologies for some simple small molecules
> but it doesn't help me now, because it doesn't support Si atoms and has a
> limit of 300 atoms per molecule (also I could get around the last problem with
> only processing a small unit cell and then multiply this cell 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.
> The problem is that even though I know how a topology file should look like in
> general (in a way that I understand what the different sections deal with and
> how the parameters are incorporated into the simulation), it doesn't help me
> in finding the parameters. I can get the bond lengths and angles from the
> structure of course, but what I lack is the force constants and atomtypes (of
> course I have O and Si in the GROMACS96 ff but no atomtype for
> siloxyl-oxygen/silison, although maybe the carboxyl-atomtypes could be
> similar), and especially the vdW parameters for non-bonded interaction (of
> course these are already there, if I use existing atom types instead of
> introducing new types for silicon bound to oxygen and vice versa).
> To sum it up: How could I obtain these force constants and vdW parameter for
> non-bonded interactions? Or has anyone some reference at hand where these
> parameters are published for SiOx-Substrates?
> I guess that I don't mind at all if the intramolecular paramters are not
> perfect because anyhow I'll fix the whole substrate by position restraints.
> What will be important is the interaction nonbonded interaction between the
> substrate and the other molecules in the simulation (hence the vdW parameters,
> right?).
>>> 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...
> I ment to construct the substrate (i.e. silicon surface) by just positioning
> single Si and O atoms (or SiO2 molecules) in an appropriate way instead of
> modelling the substrate as one big molecule. Because I guess this structure
> would not be stable in itself, I would suppose that one needs position
> restraints to keep the substrate together in such a case.
> Your thoughts on this would be much appreciated,
> Thanks,
>     Michael
>>> 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?
@Article{ Wensink2000a,
   author =       "E. J. W. Wensink and A. C. Hoffmann and
                   M. E. F. Apol and H. J. C. Berendsen",
   title =        "Properties of adsorbed water layers and the effect
                   of adsorbed layers on interparticle forces by liquid
   journal =      "Langmuir",
   year =         2000,
   volume =       16,
   pages =        "7392-7400"
@Article{ Spoel2006c,
   author =       "David {van der Spoel} and Erik J. W. Wensink and
                   Alex C. Hoffmann",
   title =        "Lifting a wet glass from a table: {A} microscopic
   journal =      "Langmuir",
   year =         2006,
   volume =       22,
   pages =        "5666-5672",
   OPTurl =               "http://dx.doi.org/10.1021/la053284f"

You can use x2top to generate a topology.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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