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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