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

Rajiv Gandhi grajiv03 at gmail.com
Thu Sep 20 08:31:06 CEST 2012

Could you tell me what is the procedure to cut the bond to produce
the photodissociation?

On Thu, Sep 20, 2012 at 3:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
> Mark
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