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

Rajiv Gandhi grajiv03 at gmail.com
Thu Sep 20 05:08:38 CEST 2012

Dear all,

Why all people cut the protein ligand bond to produce the photodissociation?

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 ?

Thanks in advance for for you any comments.

Kind regards


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