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<DIV>Dear gmx users,</DIV>
<DIV> </DIV>
<DIV>I'm fairly new to gmx and I'm using the analysis tools to understand the
persistent features of a large ensemble of conformers of an unstructured protein
restrained with PRE NMR data.</DIV>
<DIV> </DIV>
<DIV>I generated a contact map over the ensemble using the following
command</DIV>
<DIV> </DIV>
<DIV>g_mdmat -f fname.pdb -s fname.pdb -mean</DIV>
<DIV> </DIV>
<DIV>Viewing the map after converting with xpm2ps, I found a few persistent
contacts.</DIV>
<DIV> </DIV>
<DIV>I then tried to look at the minimum distance distribution for the residue
pairs that gave the closest contacts in the average contact map.</DIV>
<DIV>I used make_ndx to create selections of all atoms of the residues of
interest, then used the g_mindist with a pair of residues selected.</DIV>
<DIV> </DIV>
<DIV>g_mindist -f fname.pdb -s fname.pdb -n myindexfile.ndx</DIV>
<DIV> </DIV>
<DIV>If I average over the output of g_mindist, I do not get a value that is
near the discrete value in the g_mdmat contact map representation. Should
these values be the same? If not, why not?</DIV>
<DIV> </DIV>
<DIV>Thanks,</DIV>
<DIV>David Lowry</DIV></DIV></BODY></HTML>