[gmx-users] water layer with g_select

[Mark Abraham]

On 29/08/2012 7:43 PM, Bala subramanian wrote:
> Hi,
> 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"'

The examples that use rdist take care to define it on the previous line, 
which you haven't.

Mark

>
>
> 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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>
>