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

rajat desikan rajatdesikan at gmail.com
Sat Aug 23 21:17:47 CEST 2014

Hi Dawid,

In my understanding, a hydrogen bond is considered between one set of
hydrogen-donor-acceptor in Gromacs. So, when your water molecule flips and
its oxygen becomes the acceptor, it is considered as a different hydrogen
bond. So, the plot you have two hydrogen bonds each with differing
lifetimes, one short and the other long. I think that g_hbond takes this
into account.

There are different ways to plot the salt-bridge distances. The criteria
used by VMD makes sense to me. VMD defines a salt-bridge between two
residues if *any* oxygen of the acidic residue (Asp, Glu) falls within the
cut-off distance of *any* nitrogen of the basic residue (Arg, Lys, His).
However, the salt bridge distance is computed between the center of mass of
all the oxygen atoms in the acidic residue side chain and the center of
mass of all the nitrogen atoms in the basic residue. This distance is
different than the acceptance criteria for salt bridges (like you rightly
recognized), but is necessary since residues like Arginine have multiple
nitrogen atoms which can switch in the salt bridge formation due to thermal


On Sun, Aug 24, 2014 at 12:22 AM, Dawid das <addiw7 at googlemail.com> wrote:

> 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:
> http://www.speedyshare.com/8xHDs/Zrzut-ekranu-z-2014-08-23-19-33-45.png
> 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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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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