[gmx-users] How to carry out rigid body
x.periole at rug.nl
Thu Mar 12 15:19:51 CET 2009
In the case of Martini(CG)-derived protein simulations we use an
to connect the backbone (C-alpha) beads. This allows to control the
and dynamics of the protein.
We parameterized this EN to reproduce atomistic simulations and
with a cutoff of 0.8/0.9 nm and a force constant of 500 kJ/mol/nm2 the
could reproduce structural (rmsd) and dynamical (rmsf and large
That might help you, although I am not sure what your objects are.
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
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