[gmx-users] water layer with g_select

Bala subramanian bala.biophysics at gmail.com
Wed Aug 29 11:43:55 CEST 2012

I read the examples. I find that one example shows the usage of rdist
keyword. But i am not getting the right syntax to use it. I tried
several ways as follows to find water within .25-5 nm. Could someone
help me here.

-select 'resname SOL and within (0.25 and 0.5)  of group "Protein"'
-select 'resname SOL and rdist>=0.25 and rdist <=0.5  of group "Protein"'
-select 'resname SOL and within 0.25-0.5 of group "Protein"'
-select 'resname SOL and (rdist >=.25 and rdist <=0.5) of group "Protein" '
-select 'resname SOL and within (rdist >= 0.25 and rdist <= 0.5) of
group "Protein"'
-select 'resname SOL and within {0.25 to 0.5}  of group "Protein"'

On Tue, Aug 28, 2012 at 5:56 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 29/08/2012 1:37 AM, Bala subramanian wrote:
>> Friends,
>> I read the documentation of g_select and previous questions, but I
>> could nt find how to extract the index of water layer around the
>> protein. While i understand that i can use 'within' keyword to get
>> water layer around protein, my need is slightly different in a sense
>> that i have specify a range of distances. For instance: Water at 2.5
>> to 5.0 Ang from protein etc.
>> I tried something like within 0.25 to 0.5, within 0.25-0.5 etc, but i
>> was not successful.
> g_select -select "help examples" has some useful starting material. You want
> atoms whose distance is greater than 0.25 and less than 0.5, so ask for
> that.
> Mark
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C. Balasubramanian

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