[gmx-users] question on diffusion during MD

[Ramon Crehuet]

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?

Thanks in advance,

Ramon