[gmx-users] writing trajectory with water molecules within a distance from protein
erikm at xray.bmc.uu.se
Tue May 10 11:15:10 CEST 2011
You can use g_order for that with just a bit of additional scripting.
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
> 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.
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> Maria G.
> Technical University of Denmark
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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