[gmx-users] How to produce the photodissociation in Gromacs?

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 20 08:12:38 CEST 2012

On 20/09/2012 1:08 PM, Rajiv Gandhi wrote:
> Dear all,
> Why all people cut the protein ligand bond to produce the photodissociation?

Because MM forcefields typically assume bonds do not break or form. 
Electronic degrees of freedom are not directly considered in the model.

> For instances, In myoglobin, To simulate photodissociation of the CO
> complex, the Fe–CO bond of the
> starting structure was cut before any calculation.Fe-C bond were cut and
> instantaneously switch the heme force
> field from 6-coordinated Fe to that of the 5-coordinated Fe.
> I want to understand how we can delete this bond between Fe-CO  to induce
> the photodisssociation ?  After we cut the bond what it can do during MD
> simulation ?

If you know enough about such a system to parametrize the bonded and 
non-bonded systems, then in principle you could watch the process of 
dissociation after cleavage. But I can imagine spending 6 months to do 
that parameterization and still failing. A modelling approach that works 
nicely for simple first- and second-row elements not undergoing chemical 
reactions need not be extensible to either transition elements or reactions.


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