Ramon Crehuet wrote:
Dear gmx users,
I am running MD simulations of a tetrameric protein and as I want to
compare with neutron scattering data I need to take into account protein
diffusion implicitly. If I use /nstcomm = 1/ (default value) the
simulation (1 ns) leads to a minimal random motion (traslational and
rotational), but when using/ nstcomm = total_steps_of_the_simulation/
the protein is moving much more towards a quite defined direction. Am I
actually introducing traslational diffusion or is it an artifact?
It's an artefact. Look at comm_mode, or set nstcomm = 0 to avoid using
these algorithms.
Mark
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