Re: question on hydrogen bond

From: ehenriques_at_qui.uc.pt
Date: Mon Sep 06 2010 - 05:06:57 CDT

Hi,

"Explicit hydrogen bonds" used to be a separated term in the potential
energy for the van der Waals of atoms involved in H-bonds: it was a
10-6 wdW-term instead of the traditional 12-6. It is not used in the
current generation of CHARMM, meaning that the vdW for the hydrogens
bonds are calculated with the same regular 12-6 term as any other vdW
interactions in your system.

Elsa

Quoting Kwee Hong <joyssstan0202_at_gmail.com>:

> Hi.
>
> 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 culculated? So does that mean that I can't inspect the
> hydrogen bonding which is important in stabilizing my protein throughout the
> simulation?
>
> Thanks.
>
> Regards,
> Joyce
>

-- 
Elsa S. Henriques                     e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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