[gmx-users] Hydrogen bond breaking process

[Peter C. Lai]

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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