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
syntax).
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:
GRO=indo.1.2.6.5us.gro;
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,
Chris.
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