[gmx-users] Re: g_select: selection file problem

[Oleksandr Sushko]

Teemu Murtola-3 wrote
> Hi,
> 
> On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko
> <

> o.sushko at .ac

> >wrote:
> 
>> I'm want to analyse stratified layers of water around protein,
>> so I provide next selection file to g_select:
> 
> [clip]
>> (shell2 is supposed to be a layer of whole water molecules from the layer
>> 3 to 4 A)
>> but it doesn't work correctly, moreover it even provides different
>> results
>> when just changing
>> the order in 3rd line (shell2 = shell1 and shell), which shouldn't be the
>> case.
>> Interestingly, 1st and 2nd line separately works correctly.
>>
>> Even more interesting the next selection file works perfectly fine
>> (regardless the order in 3rd line):
>> [clip]
>>
> 
> Thanks for reporting this, this is clearly a bug. I have filed
> http://redmine.gromacs.org/issues/1216 with some explanation of what
> triggers the bug.
> 
> (this also provides a layer between 3 and 4 A from protein, but some
>> molecules are represented only by 1 or 2 atoms, which I want to avoid,
>> that's why I'm using 'same residue as')
>>
> 
> There is probably no way to get exactly your condition before the bug is
> fixed, but if you are OK with a slightly altered condition, you can do,
> for
> example, this (haven't tested, but should work):
> 
> shell = group "SOL" and res_com within 0.4 of group "protein";
> shell1 = group "SOL" and not res_com within 0.3 of group "protein";
> shell2 = shell and shell1;
> shell2;
> 
> Best regards,
> Teemu
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your suggestion with res_com works fine,
although it results in less molecules for same shell compared to 'same
residue as',
but still keeps whole molecules in selection, which suits me.
thanks a lot,
Oleksandr



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