I am not sure what is going on in this case. You could try:
which g_spatial
to see what is being picked up. You could also try to move the
g_spatial executable to its own directory and then execute g_spatial
from that path:
/new/path/to/executable/g_spatial -h
ls /new/path/to/executable/g_spatial
g_spatial
Otherwise I am not sure what is going on. Are you sure that you didn't
compile g_cluster under the name g_spatial by accident?
Chris.
-- original message --
HI Chris
I followed the steps below and when i tried to run g_spatial it
executed g_cluster instead. Even when i do g_spatial -h it looks like
its being overwritten by g_cluster
1.I used make_ndx to create a group containing the atoms around which i want
the SDF
2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur
compact -pbc none
3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans
4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx
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