[gmx-users] Distance matrix of the trajectory
hmkvsri at gmail.com
Fri Jan 25 11:08:58 CET 2013
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?
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