[gmx-users] writing trajectory with water molecules within a distance from protein

[Erik Marklund]

You can use g_order for that with just a bit of additional scripting.

Erik

maria goranovic skrev 2011-05-10 09.17:
> So, one can probably do this using a simple script?
>
> for each frame
>
> make index file of water molecules within 0.5 nm using g_select
> extract frame based on above selection
>
> done
> concatenate frames
>
> The only problem with the above would be that the number of water 
> molecules selected might change with each frame. Is there a way of 
> choosing the closest, say, 1000 water molecules using g_select
>
> On Tue, May 10, 2011 at 12:28 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 10/05/2011 12:50 AM, maria goranovic wrote:
>
>         Dear experts
>
>         I have a protein simulation in a water box. I now want to
>         write a trajectory containing only the protein, and water
>         molecules within 5 Angstroms of the protein, with the water
>         list being updated each time step. How can one do this?
>         Appreciate the help
>
>
>     g_select is useful for "dynamic" selections of this type. g_select
>     -select "help" can give examples and such.
>
>     I'd hope it's been designed so that then using trjconv to extract
>     such selections works, but I can't think how, having not ever tried.
>
>     Mark
>     -- 
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>
>
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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