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

maria goranovic mariagoranovic at gmail.com
Tue May 10 09:17:00 CEST 2011

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>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
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