[gmx-users] water layer with g_select

[Mark Abraham]

On 08/29/2012 09:33 PM, Bala subramanian wrote:
> Hi Mark,
> Thanks. I tried defining the rdist in several ways and each time i get
> an error as follows, and the last definition of rdist is infact very
> similar to what is shown in examples.Could you suggest what is the
> mistake i'm doing here.

You're still not following the example. You have to measure a distance 
from a point to a point, and (for example) your first attempt is leaving 
both definitions vague. The example uses "res_com distance from com..." 
for a reason.

g_select -select 'rdist = res_com distance from com of group Protein; 
resname SOL and rdist >= 0.25 and rdist <= .5'

Mark

>
> selection parser: invalid expression value for parameter 'from'
>
> Definitions of rdist. My protein contains 16 alanine residues in water box.
>
> rdist = distance from atom of group "Protein"; resname SOL and rdist
>> =0.2 and rdist <=0.5
> rdist = distance from atom of resnr 1 to 16; resname SOL and rdist
>> =0.25 and rdist <=0.5
> rdist = res_com distance from atom of resnr 1 to 16; resname SOL and
> rdist >=0.25 and rdist <=0.5
> rdist = atom distance from atom of resname ALA; resname SOL and rdist
>> =0.25 and rdist <=0.5
> rdist = res_com distance from atom of resname ALA; resname SOL and
> rdist >=0.25 and rdist <=0.5
>
> thanks
>
> On Wed, Aug 29, 2012 at 11:59 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>> 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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>
>