I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial displacement. this will give rise to a non-realistic MSD. is g_msd intelligent enough to avoid this artificial displacement?
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