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:
> 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
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.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:30 CST