[gmx-users] is it possible?

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 30 10:55:05 CET 2012

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.


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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

More information about the gromacs.org_gmx-users mailing list