In the case of Martini(CG)-derived protein simulations we use an
elastic network
to connect the backbone (C-alpha) beads. This allows to control the
conformation
and dynamics of the protein.
We parameterized this EN to reproduce atomistic simulations and
observed that
with a cutoff of 0.8/0.9 nm and a force constant of 500 kJ/mol/nm2 the
CG-protein
could reproduce structural (rmsd) and dynamical (rmsf and large
amplitude collective
motion) properties.
That might help you, although I am not sure what your objects are.
XAvier.
On Mar 12, 2009, at 2:47 PM, lammps lammps wrote:
Hi everyone,
I want to peform CG-MDs with gromacs. In my system, there are some
rigid bodies which are composed by hundreds of LJ atoms. Atoms of
each rigid body move together in LJ water solution.
How can I deal with it? Any suggestion is appreciated. Thanks in
advance.
--
wende
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