[gmx-users] ELNEDIN disulfide bridge

[XAvier Periole]

the force constant in MArtini is 5000 kJ/mol/nm^2

On May 10, 2010, at 4:21 PM, XAvier Periole wrote:

>
> There no specific term associated with di-sulfide bridge in ElNeDyn.  
> It is
> however recommended to use a cutoff for the Elastic network of 0.9 nm.
> The two Backbone beads are certainly within that distance so it is  
> pretty
> save.
>
> Nevertheless to include the disulfide bridge explicitly you should  
> add a
> bond in your topology between the two side chain beads. The same force
> constant as in regular Martini should be used. The changes between  
> ElNeDyn and
> Martini relate to other things.
>
> XAvier.
>
> On May 10, 2010, at 4:03 PM, Lea Thøgersen wrote:
>
>> I am trying to set up an ELNEDIN simulation of a protein which  
>> contain a disulfide bridge. As all the bonded interactions are  
>> changed compared to the MARTINI force field, I do not know how the  
>> parameters should be set for this bond, as it would seem  
>> unreasonable simply to use the MARTINI values.
>>
>> Has anyone reparameterised the disulfide bond for the ELNEDIN  
>> model, or have an idea of how I should proceed?
>>
>> Regards
>> Lea
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