[gmx-developers] g_select empty selection

Michel Cuendet michel.cuendet at isb-sib.ch
Fri Feb 26 21:19:43 CET 2010

Hi all,

I think g_select is a great tool that had been missing in gromacs for a
long time! I however stumbled on a weird behavior. I was trying to count
waters involved in the interface between chainA and chainB, using the
following input file:

waterO = group SOL and name OW;
heavy1 = group ChainA and group "Protein-H";
heavy2 = group ChainB and group "Protein-H";
inter = waterO and within 0.35 of heavy1 and within 0.35 of heavy2;
notinter = waterO and not inter;
test = notinter and heavy1;

The goal was to use the non-interacting waters stored in notinter to do
some more elaborate selections. But if notinter is used further in the
input file (as with the dummy line "test = notinter and heavy1"), the
selection notinter becomes empty. So the input file above would give
zero elements for notinter. If you remove the last line, the same input
file gives the correct number of elements in notinter.

Note that I am not using the very last git version, but from the change
log it doesn't seem that g_select has been updated since. Note also that
the webpage to search the gmx-developers list is broken.


PS: It would be great to be able to use in g_select a selection
criterion similar to the one in g_hbond !

More information about the gromacs.org_gmx-developers mailing list