[gmx-users] Hydrogen bond breaking process
jalemkul at vt.edu
Mon Sep 3 03:48:25 CEST 2012
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.
> 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
>> 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 A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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