[gmx-users] Distance matrix of the trajectory

Kavyashree M hmkvsri at gmail.com
Fri Jan 25 11:08:58 CET 2013

Dear users,
While calculating the distance matrix using g_mdmat, with -no option,
it gives an xvg output pertaining the total, mean etc contacts of the
within 1.5Ang in the trajectory.
I calculated the same for a single frame (or pdb file)

#res    ratio  tot      mean  natm  mean/atm
  1     1.000  640   640.000   19    33.684
  2     1.000  530   530.000   17    31.176
  3     1.000  805   805.000   22    36.591
  4     1.000  571   571.000   17    33.588

I am little doubtful about the number under total. Does this mean that the
atoms of that residue has total of 640 contacts (in one frame)?

Are there any otherway to get contact map for the whole trajectory where we
can mention min and max cut-off distance?

Thank you

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