I'm trying a coarse-grained simulation with three beads
representing the backbone structure of each residue. However, it's
difficult to get the LJ parameters for -NH- and -CO- . Could anyone
possibly know some work on this?
Well, there is no magic parameters for NH or CO for a Coarse-grain
simulation!
These would be effective interaction and therefore depend entirely of
the rest
of the interaction you are using!
You'll have to parameterize them to reproduce data that you think
relevant.
It is a very vague answer, sorry, but your question suggests that you
should
try some literature on the subject force field parameterization and
coarse-graining.
hope this helps.
XAvier.
Thanks in advance.
Cristty
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