[gmx-users] Re: gmx-users Digest, Vol 55, Issue 51

Gadzikano Munyuki Gadzikano.Munyuki at uct.ac.za
Mon Nov 10 09:59:39 CET 2008

I have checked the source code and it looks like g_spatial has been replaced by g_cluster.I got the code below under g_spatial.c

/* This is just a wrapper binary.
* The code that used to be in g_cluster.c is now in gmx_cluster.c,
* where the old main function is called gmx_cluster().
main(int argc, char *argv[])
  return 0;


-- original message --

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

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?


-- 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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