[gmx-users] make_ndx: execlude one group from another

Mark Abraham mark.abraham at anu.edu.au
Fri Sep 24 11:17:59 CEST 2010

----- Original Message -----
From: Thomas Schlesier <schlesi at uni-mainz.de>
Date: Friday, September 24, 2010 18:43
Subject: [gmx-users] make_ndx: execlude one group from another
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>

> Hi all,
> I'm trying to execlude all atoms of group 2 (140 atoms) from 
> group 1 (300 atoms), so that i have a new group 3 (with 160 atoms).
> | is for merging with OR
> & for merging with AND
> so ! should be for merging with NOT

No. "NOT" is a unary operator, which (in this case) negates the sense of a set. You can be in A or NOT in A. In English we might say "in B not A" which makes sense (sloppily), but there's an implicit AND binary operator to combine the two operands, viz "in B AND NOT in A". make_ndx requires the precise version.


> But i tried
> 1 ! 2
> 2 ! 1
> but in both cases make_ndx complains about syntax errors
> Syntax error: "! 1" ; or same with "! 2"
> To use NOT instead of ! doesn't work. But using AND insted of & 
> also doesn't work.
> So what's the right command for merging with the NOT option?
> Greetings Thomas
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