[gmx-users] Re: Gold layers

[David]

On Wed, 2004-03-17 at 17:30, Keta Jones wrote:
> Dear Dr Spoel,
> 
> many many thanks for your help.still I am struggling
> with that issue.I am also very new to Gromacs.To be
> more specific I want to study a peptide between two
> walls of hydrated gold surface.Each wall has five
> layers of gold. Outer layer is hydrogenated.
> 
> Au Au Au Au Au-h   peptide  h-Au Au Au Au Au
> Au Au Au Au Au-h   peptide  h-Au Au Au Au Au
> Au Au Au Au Au-h   peptide  h-Au Au Au Au Au
> Au Au Au Au Au-h   peptide  h-Au Au Au Au Au
> Au Au Au Au Au-h   peptide  h-Au Au Au Au Au
> Au Au Au Au Au-h   peptide  h-Au Au Au Au Au
> 
> Is this type of system can be handled by
> Gromacs.Please tell me how I can generate the PDb
> files for this system.I know the inter layer Gold
> distances and distance between h-Au.I have the PDB
> file for peptide.
> With this background How canI proceed.

Probably you want to generate a single slab of gold with hydrogens on
either side, and then use periodic boundary conditions. You should start
with this before adding the peptide. Since you have to create an
"infinite molecule" you will have to use the x2top program to create a
topology once you have the coordinates. The gold coordinates you can
probably generate using genconf, once you have a suitable "unit cell",
that should look something like (one or two of these):

h-Au Au Au Au Au Au Au Au Au Au-h


Check out the mailing-list archives for x2top use once you have the
coords.

> 
> Further help will be appreciated.
> regards,
> keta
> 
> =====
> Keta
> **************************************************************************************
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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