[gmx-users] g_mindist and g_mdmat

SUSAN VARNUM huskyrunnr at msn.com
Wed Mar 14 22:21:27 CET 2007

Dear gmx users,

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.

I generated a contact map over the ensemble using the following command

g_mdmat -f fname.pdb -s fname.pdb -mean

Viewing the map after converting with xpm2ps, I found a few persistent contacts.

I then tried to look at the minimum distance distribution for the residue pairs that gave the closest contacts in the average contact map.
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.

g_mindist -f fname.pdb -s fname.pdb -n myindexfile.ndx

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?

David Lowry
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