[gmx-users] Re: PBC problems when creating water layer around protein on an XTC trajectory

[Tsjerk Wassenaar]

Hi Marc,

-pbc closest_to_any_atom_of_the_reference_group  (eg protein in our case)

That's exactly what I've implemented in trjconv, though I made the
option a bit shorter ;) and in my newer version it's actually an
option to -ur (which allows you to use -pbc whole). I'll send you the
code off list later today if you'd like. In the future I'll also clean
up the code and contribute it to Gromacs...

Cheers,

Tsjerk

On 7/27/05, Xavier Periole <x.periole at rug.nl> wrote:
> Marc Baaden wrote:
> 
> >Hi,
> >
> >we are currently analysing some trajectories where we would like to look
> >at the hydration shell(s) of the simulated protein. We have already
> treated
> >the system with trjconv and trjorder to obtain the centered protein with
> its
> >20000 closest water molecules.
> >
> >What troubles us is trying to get the "visually" correct water shell,
> which
> >is problematic because the protein is elongated, and using its center of
> mass
> >as reference point (as in -pbc cluster) does not systematically yield the
> >right periodic copy of the waters. In some cases one would want the water
> one
> >periodic box above or to the side. In fact to have the right result,
> several
> >periodic copies need to be considered.
> >
> >The missing option in trjconv that could solve this would be :
> >
> > -pbc closest_to_any_atom_of_the_reference_group  (eg protein in our case)
> >
> >because the com of the protein is not the right reference for the waters
> >at the edges.
> >
> >  
> >
> I am not sure I completely understand your problem, but the solution I 
> would give is that
> based on the trajectory you already ordered and selected the 20000 
> closest waters, you can
> get an extimate of the number of water molecules in the first shell 
> (using any program giving
> you the possibility to select with a distance criterion). Then you can 
> generate a index file
> that will contain a group defined ans the residue from the first water 
> molecule + the number
> of molecules. Then use trjconv on the ordered trajectory and print only 
> the protein and this
> group of N water molecules.
> 
> Hope this helps,
> XAvier
> 
> -- 
> ----------------------------------
>  Xavier Periole - Ph.D.
> 
>  Dept. of Biophysical Chemistry / MD Group   
>  Univ. of Groningen
>  Nijenborgh 4
>  9747 AG Groningen
>  The Netherlands
>  
>  Tel: +31-503634329
>  Fax: +31-503634800
>  email: x.periole at rug.nl
>  web-page: http://md.chem.rug.nl/~periole
> ----------------------------------
> 
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