[gmx-users] coarse-grained simulation of proteins

[XAvier Periole]

> 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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