[gmx-users] Re: Gold layers

[Keta Jones]

Dear Dr David,

Thanks for your support.I came through the genconf
keyword.I realize that "genconf multiplies a given
coordinate file by simply stacking them on top of each
other".but I am struggling how to start with whn I d
nonot have any initial co-ordinates.I hope if I have
some initial co-ordinates then only I can use genconf
for my system.

thanks
regards,
keta

--- David <spoel at xray.bmc.uu.se> wrote:
> 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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=====
Keta
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