[From nobody Thu Nov 14 11:50:14 2013
Date: Mon, 10 Nov 2008 10:59:39 +0200
From: "Gadzikano Munyuki" <Gadzikano.Munyuki@uct.ac.za>
To: <gmx-users@gromacs.org>
Subject: Re: gmx-users Digest, Vol 55, Issue 51
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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().
*/
int
main(int argc, char *argv[])
{
  gmx_cluster(argc,argv);
  return 0;
}


Gadzikano

-- 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 =20
g_spatial executable to its own directory and then execute g_spatial =20
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 =20
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 =20
executed g_cluster instead. Even when i do g_spatial -h it looks like =20
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 =20
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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