[gmx-users] g_select: selection file problem

Oleksandr Sushko o.sushko at eecs.qmul.ac.uk
Thu Apr 4 21:01:14 CEST 2013


Dear Gromacs users,
I'd appreciate any help in rather strange problem.

I'm want to analyse stratified layers of water around protein,
so I provide next selection file to g_select:
*
**shell = group "SOL" and same residue as within 0.4 of group "protein"**;**
**shell1 = group "SOL" and same residue as not within 0.3 of group 
"protein";**
**shell2 = shell and shell1;**
**shell2;*

(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):

*shell = group "SOL" and within 0.4 of group "protein"**;**
**shell1 = group "SOL" and not within 0.3 of group "protein";**
**shell2 = shell and shell1;**
**shell2;*

(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')

Does anybody have a clue of what can be the reason, I run out of ideas.

thanks in advance,
Oleksandr Sushko



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