[gmx-users] is it possible?

[Mark Abraham]

Not easily - a complex geometric criterion is needed to define a
multi-molecule H-bonding bridge.

g_hbond can probably be made to do the simple case with 1 bridging water,
but anything more complex than that will need the functionality of g_select.

Mark

On Fri, Nov 30, 2012 at 10:31 AM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
>   I've got two polar residues which make H-bond directly. However, I found
> that this Hbond can be broken by solvent molecules: sometimes there is 1
> water molecule stucked in the middle during the simulation and sometimes 2
> even 3. But those water molecules can bridge this two residues through
> Hbonds. So I am just wondering is it possible in Gromacs to make statstics
> on the number of water molecule stuck within this  two residues?
>
> thank you very much.
> Albert
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