[gmx-users] Re: PBC problems when creating water layer around protein on an XTC trajectory
tsjerkw at gmail.com
Thu Jul 28 10:33:24 CEST 2005
-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:
> >we are currently analysing some trajectories where we would like to look
> >at the hydration shell(s) of the simulated protein. We have already
> >the system with trjconv and trjorder to obtain the centered protein with
> >20000 closest water molecules.
> >What troubles us is trying to get the "visually" correct water shell,
> >is problematic because the protein is elongated, and using its center of
> >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
> >periodic box above or to the side. In fact to have the right result,
> >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 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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