[gmx-users] Re: Gold layers

[David van der Spoel]

On Fri, 2004-03-19 at 06:18, Keta Jones wrote:
> 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.
> 
Since your gold unitcell probably contains only one or two atoms you can
type it in manually.


> 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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-- 
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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