[gmx-users] File editing - only one layer of water around a molecule

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 13 11:51:27 CEST 2012

On 13/04/2012 7:29 PM, Lara Bunte wrote:
> I read g_select -select 'help all' and I understand nothing of that.
> In general one have a molecule (valences closed by hydrogen) and a 
> water box around it. How to select only the protein with the first 
> water layers, say one layer?
> Please give me an example how to do this with gromacs. I read the 
> examples in g_select -select 'help all' and I have no Idea what they 
> are talking about.

Surely you can see that the example

All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):
   "Close to protein" resname LIG and within 0.5 of group "Protein"

is very similar to what would be needed for all water residues within 
some distance of your solute.

VMD uses a similar approach. BioPython probably likewise. There's no 
genie going to wave the magic create-a-layer wand. You need to learn how 
to create a layer from a definition that suits you, because you'll 
probably have to vary that definition until you're happy with the outcome.


> Thanks for help
> Greetings
> Lara
> ------------------------------------------------------------------------
> *Von:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *An:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Gesendet:* 19:26 Mittwoch, 11.April 2012
> *Betreff:* Re: [gmx-users] File editing - only one layer of water 
> around a molecule
> On 12/04/2012 3:24 AM, Justin A. Lemkul wrote:
> >
> >
> > Lara Bunte wrote:
> >> Could you please give how g_select is used?
> Reading g_select -h might have led you to try g_select -select 'help'
> >> Is there a tutorial for that?
> >>
> >
> > g_select -select 'help all'
> >
> > The information contained therein is very extensive, so be sure to 
> read it thoroughly.  It will fill several terminal windows explaining 
> the syntax and providing examples.
> ... and search Google for some examples.
> Mark
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