[gmx-users] diffusion coefficient

[Ruhollah Moussavi-Baygi]

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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