[gmx-users] How to carry out rigid body

XAvier Periole 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  
elastic network
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  
observed that
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  
amplitude collective
motion) properties.

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  
> advance.
> -- 
> wende
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