[gmx-users] about g_hbond

[Anton Feenstra]

Alan Wilter Sousa da Silva wrote:
> To myself
> 
> I found that hbmap.xpm plots the information about water molecules
> intermediating H-bonds.  However, it leads me to another question: what is
> the difference between '(blue) Inserted' and '(pink) Present & Inserted'?

Inserted means the 'original' h-bond was broken, and now a water molecule
sits in between the donor and acceptor of the 'original' bond.
Present & Inserted means the 'original' bond is still present also,
involvind a triplet of bifurcated h-bonds, i.e. from 'original' donor to
'original' acceptor and the water molecule, and from the water to the
'original' acceptor.

If you run g_hbond only once on your trajectory, it will only find insertions
*after* a h-bond was present in your solute molecule. You could run it twice
to get first a .ndx file with all the possible D-H-A triplets, and then get
all insertions for them in a second run (described in the manual also, IIRC).

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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