[gmx-users] g_select is pretty fantastic

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue May 3 04:48:44 CEST 2011

Dear g_select developers:

This is a shout out of thanks for this new tool, which I find very useful.

For users who have not played around with this, I'd suggest trying it  
(especially if you are already familiar with VMD-style selection  

I want to make special thanks for the VMD-style selection language,  
which avoids us all having to learn yet another protocol. I would  
suggest direct interaction between the g_select developers and the VMD  
developers to bring this into lock-step over the coming years (perhaps  
a universal selection syntax?). Another suggestion is that I only  
realized that the syntax is essentially a VMD-syntax by trying it out  
(there is no documentation that mentions this). I'm thus not sure how  
overlapping the syntaxes really are, but would request that they  
become fully-overlapping over time and that the current possibilities  
are mentioned in the help information.

Another important note is that you need to supply a .ndx file from a  
simple run through make_ndx to get things to work like "group  
Protein". I think it was a good decision to wall-off the creation of  
standard selection groups (make_ndx) from the g_select program, but I  
think that this fact would be useful in the documentation.

To be more explicit about the possibilities, one can do things like:

echo -e "aP8\nq\n" | make_ndx -f ${GRO} -o initial.ndx;
g_select -f ${GRO} -n initial.ndx -on select.ndx -select "same residue  
as group P8 and within 1 of group Protein" -s full.tpr;

Pretty cool.

Thanks again,

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