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" <[EMAIL PROTECTED]>
To: <gmx-users@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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
