[gmx-users] writing trajectory with water molecules within a distance from protein
Mark.Abraham at anu.edu.au
Tue May 10 00:28:46 CEST 2011
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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