[gmx-users] Photodissociation through MD

[francesco oteri]

Hi,
could you try to use the Morse potential for this bond.
As far as I know, the parameters can be directly obatined forml the armonic
potential expression.

Francesco

2012/9/21 Mark Abraham <Mark.Abraham at anu.edu.au>

> 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
>>
>
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-- 
Cordiali saluti, Dr.Oteri Francesco