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.abra...@anu.edu.au <mailto:mark.abra...@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
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Erik Marklund, PhD student
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