[gmx-users] Hydrogen bond breaking process

[Rajiv Gandhi]

Is there any publication regarding this Fe-CO covalent bond breaking ?
Actually in experimental techniques, the bond between Fe-CO in myoglobin
gets broken in100 ps time scale. Is't possible to do this process by QM/MM
methods or ReaxFF? Please need an advice. I haven't have any
prior knowledge on this, Thanks in advance.

On Mon, Sep 3, 2012 at 2:51 PM, Peter C. Lai <pcl at uab.edu> wrote:

> Well there is always ReaxFF. You'd still have to use QM/MM to parameterize
> the various states though.
>
> On 2012-09-02 09:48:25PM -0400, Justin Lemkul wrote:
> >
> >
> > On 9/2/12 9:42 PM, Rajiv Gandhi wrote:
> > > Could you tell me how can i perform for coordinate covalent bond
> breaking
> > > and forming between Fe-CO in myoglobin. I guess, it has been already
> done
> > > by some groups. If possible can you send me journals related to this.
> >
> > You can't break and form bonds in classical MD.  That's an exercise for
> QM/MM.
> > There are plenty of articles out there, a Google search would turn up
> hundreds,
> > maybe even some directly related to what you want to do.
> >
> > -Justin
> >
> > > Thanks.
> > >
> > > On Mon, Sep 3, 2012 at 8:55 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >>
> > >>
> > >> On 8/31/12 10:43 PM, Rajiv Gandhi wrote:
> > >>
> > >>> Can you tell me "how to predict the Hydrogen bond breaking process
> (For
> > >>> example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD
> > >>> simulation?
> > >>>
> > >>>
> > >> There is no hydrogen bonding in a Fe-CO interaction.  That is a
> coordinate
> > >> covalent bond.  If you want to study hydrogen bonds breaking and
> forming in
> > >> protein structures, the pull code may be useful.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==============================**==========
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Research Scientist
> > >> Department of Biochemistry
> > >> Virginia Tech
> > >> Blacksburg, VA
> > >> jalemkul[at]vt.edu | (540) 231-9080
> > >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >>
> > >> ==============================**==========
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> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
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> Peter C. Lai                    | University of Alabama-Birmingham
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-- 
Kind regards

Rajiv