[gmx-users] Photodissociation through MD

[Mark Abraham]

On 21/09/2012 11:35 AM, 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?.

By not making it in your topology. Whatever procedure you follow for 
making the other Fe-C interactions needs to differ from the one you wish 
to model the cleaved bond.

Mark

> 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.
>
>
> Sincerely
>
> Rajiv