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
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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