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

[Mark Abraham]

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