Hi Mark,
Thank you for your reply.
I understand now.
Sincerely yours,
Hsin-Lin
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?
Yes it is.
Not sure about g_msd, but you can take care of it yourself with a
workflow derived from the information here
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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