[gmx-users] Photodissociation through MD

Justin Lemkul jalemkul at vt.edu
Fri Sep 21 03:45:43 CEST 2012

On 9/20/12 9:35 PM, Rajiv Gandhi wrote:
> Dear all gromacs users,
> In myoglobin system, how we can cut the bond between Fe-C to produce the
> photodissociation through MD?.
> I have seen there are number of studies over photodissociation and also
> I believe that people have used their appropriate parameterization files to
> cut these bond.
> I am struct with this parameter and cutting bond process. It would be
> really appreciated if anyone can give some suggestion/information about
> this. Thanks a lot.

Bonds cannot be broken or formed in classical MD.  That process is more suited 
to QM/MM type calculations.  Certainly the papers you have read provide 
methodology, and if you have specific questions on what has been done, it would 
likely be more efficient to contact the corresponding author(s) of those papers 



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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