[gmx-users] Hydrogen bond breaking process

[Justin Lemkul]

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

========================================