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...
-Justin
Any comments/suggestions , anyone?
Thanks,
Michael
On Tue, Jul 15, 2008 at 9:37 AM, Michael Hirtz <[EMAIL PROTECTED]
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
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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
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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