[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

gi, Comment by davidvanderspoel: diffusion coefficient On 2011-12-09 08:34, Mark Abraham wrote: > On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: >> I want to calculate the diffusion coefficient of a small polypeptide >> with g_msd (see here >> http://www.gromacs.org/**Docume

[gmx-users] diffusion coefficient

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 di