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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jul 28 10:33:24 CEST 2005

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...



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
> ----------------------------------
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list