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?
-- 
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to