From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 06 2010 - 04:08:32 CDT
On Sun, Sep 5, 2010 at 11:40 PM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:
> Hi.
joyce,
> In the namd-tutorial-unix.pdf, it mentioned that explicit hydrogen bond
> terms are no longer present in the CHARMM force field and are therefore not
> calculated by NAMD. Does this mean that throughout the simulation, hydrogen
> bonding are not calculated? So does that mean that I can't inspect the
hydrogen bonds are a phenomenological description and thus
technically a not an easily identifiable term for a force field.
they are more a "side effect" of the charge distribution and
geometry of groups involving hydrogens bound to certain atoms
(h-bond donors) and their counter parts (h-bond acceptors).
> hydrogen bonding which is important in stabilizing my protein throughout the
> simulation?
of course this is possible. you'll just have to follow one of
the commonly used (geometrical) definitions of hydrogen
bonds to identify those interactions. but since the definition
of a hydrogen-bond is a phenomenological one, you have
to apply a certain amount of care to not over-interpret the
absolute numbers. but rather argue with increase/decrease.
please have a look into the literature. there have been lots
of discussions about what is the best way to describe and
define a hydrogen bond, particularly in bulk water, where
researchers tend to be a bit religious about things.
cheers,
axel.
>
> Thanks.
>
> Regards,
> Joyce
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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