[gmx-users] water layer with g_select

[Bala subramanian]

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.

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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>>
>>
>>
>
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-- 
C. Balasubramanian