[gmx-users] Selecting atom indices of residues whose centers of mass match a position range

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 5 23:13:52 CEST 2012

On 6/5/12 2:55 PM, Andrew DeYoung wrote:
> Hi,
> I would like to use g_select_d to generate an index file containing the
> atoms of BF4 residues whose centers of mass are in the range z<12.24 nm.  I
> have tried the following:
> g_select -f traj.xtc -s topol.tpr -select 'resname BF4 and res_com and
> z<12.24' -on output.ndx
> But the selection syntax is incorrect.  Can you please help me?

Is there a specific error you're getting?  I think the source of the problem 
(guessing that it's just a generic syntax error) is the incorrect use of the 
res_com keyword.  Referring to the examples in the g_select help, it should be 
used something like:

'res_com of resname BF4 and z<12.24'

Note that when using res_com selection, you cannot output an index group; in 
that case you need to select based on atoms only, which are written to the index 
file.  If you're looking to write out the atoms of any residue with an atom 
below a certain z-value, the selection is simply:

'resname BF4 and z<12.24'

Selecting based on a COM below a certain z coordinate value will be more 
complex, and I'm afraid I don't know the syntax to pull that off.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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