[gmx-users] hbond hydroxyl oxygen, both acceptor and donor?

[Jeremy T First]

Hello,

I am attempting to quantify the amount of hydrogen bonding environment a
certain residue experiences during the course of a simulation. To do this,
I am using gmx hbond to plot the number of hydrogen bonds between the
solvent (water) and the hydroxyl oxygen of the residue as a function of
simulation time.

According to the help information for gmx hbond, hydroxyl oxygens are
classified as hydrogen bond donors. When I select this oxygen and the Water
group in gmx hbond, gromacs finds one less donor than acceptor, leading me
to believe that the hydroxyl oxygen is classified only as a donor, and not
also as an acceptor.

Many frames of my simulation show the hydroxyl oxygen (as calculated by
VMD) donating and accepting a hydrogen bond, but gmx hbond only reports 1
hydrogen bond for the frame.

Is there any reason that a hydroxyl oxygen can not simultaneously donate
and accept a hydrogen bond? If not, is there a way to let gromacs allow the
hydroxyl oxygen to be an acceptor as well?

Any help would be greatly appreciated!

Jeremy First
Webb Research Group
University of Texas at Austin
Jeremy_First at utexas.edu