[gmx-users] Plotting hydrogen bonds and salt bridges.

Dawid das addiw7 at googlemail.com
Sat Aug 23 20:52:44 CEST 2014

Dear Gromacs experts,

This time I have a question not regarding Gromacs itself but rather MD
analysis in general. Let's say that I want to plot the distance between
water and atom of an amino acid residue forming hydrogen bond. Now, how can
I do it when water is donor of this h-bond and water molecule flips during
the simulation so that the acutal donor changes? If you don't get me, have
a look at this screenshot:


These two plots display distance between one residue atom and two different
hydrogen atoms of the same water molecule. Now I think you understand what
I mean. So, is it okay to leave it like this to show that there is constant
h-bond between this water residue and amino acid residue? Or should I plot
it differently?

Now, I have similar question regarding salt bridges. Let's say there is
salt bridge between one atom  carrying negative charge and arginine
residue. So how to plot distance between arginine side chain and this
perticular atom? Which atom(s) of arginine should I take?

Thank you,

Dawid Grabarek

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