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--- Begin Message ---I have checked the source code and it looks like g_spatial has been replaced by g_cluster.I got the code below under g_spatial.c /* This is just a wrapper binary.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 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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