[gmx-users] Extracting the water molecules in hydration layer

Xavier Periole X.Periole at rug.nl
Tue Nov 25 17:00:00 CET 2008

On Tue, 25 Nov 2008 20:39:37 +0530
  "Suman Chakrabarty" <suman at sscu.iisc.ernet.in> wrote:
> Dear all,
> is there an easy way to extract only the water molecules in the
> hydration layer/shell around the protein/polymer chain? I need them
> both for visualization of the trajectory and some analysis.
trjorder would order the solvent based on their distance to the
protein. Then you can use an index to generate a trajectory with only
XX water molecules ..
> I can do this by writing my own program alright, but I wanted to know
> if there is any in-built prescription within gromacs. I am not being
> able to find it.
> Thanks,
> Suman.
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XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands

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