[gmx-users] g_hbond -contact option

Erik Marklund erikm at xray.bmc.uu.se
Wed Nov 22 12:04:59 CET 2006

If I'm not mistaken, g_dist deals with the center of mass of two groups, 
wheras g_hbond -contact is all about the contacts of individual atoms 
belonging to the two (or one) groups. g_hbond -contact acts just like 
g_hbond does without the -contact flag, except it ingores the angle 
criterion for hydrogen bonds. There is now also the option of providing a 
second distance for assuming a two step interaction process:

A + B <=> A- - -B <=> AB,

where the middle state is the two species being within the longer, but not 
within the shorter range (for example B being in the second coordination 
shell of A). This resembles the hydrogen bond kinetics assumed for the 
calculations of rate constants of hydrogen bonding in g_hbond, which is why 
the kinetics of the contacts may also be calculated using hte same scheme 
when two distances are provided to the program.

If you are about to use the -contact flag I strongly suggest you make sure 
you have the latest gromax version installed, since it contains some 
important bugfixes for the contact analysis. The -r2 option also requires 
the latest version.

/Erik Marklund

----- Original Message ----- 
From: "andrea carotti" <andcar at chimfarm.unipg.it>
To: <gmx-users at gromacs.org>
Sent: Wednesday, November 22, 2006 10:46 AM
Subject: [gmx-users] g_hbond -contact option

> Hi all,
> I have found this interesting option in g_hbond, and I would like to
> know something more about it. How does it work? Which is the difference
> with other tools like g_dist?
> Thanks to all
> Andrea
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