[gmx-users] Inconsistency in g_dist calculation

sunita at chem.iitb.ac.in sunita at chem.iitb.ac.in
Tue Nov 16 07:16:17 CET 2004

Dear gmx-users,

I have calculated the distance between C-alpha atoms of the first and last
residue of the peptide. The graph should decrease from high value to low
value since it is the end to end distance of the extended peptide.But what
I found is  that, during the initial 57 ps the distance is 3 nm and but
just after this it rises to 3.6 nm.

Then I calculated the distace directly from the VMD by selecting the
C-alpha atoms and then scale its x-axis to ps and y-axis to nm.When I
overlaid both the .xvg files, I found that except initial 82 ps, it
matched perfectly.

Why I am getting such inconsistency while calculating the g_dist (3.1.4).

I tried to send .xvg file of both these graphs. But due to file size I
could not able to send it.So I am sending the .jpg file with two graphs

Any suggestion is highly appreciated.

Best Regards,
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