[gmx-users] So how is the terminal methyl order parameter calculated, and about unsaturated carbons ?

[himanshu khandelia]

Hi,

As I understand it, g_order does not report the order parameter for
the terminal methyl carbon because the C-H bond is missing for united
atoms. So, how do people calculate the order parameter for the
terminal methyl atom from GROMACS simulations? I see it reported in
articles all the time. Could not find anything specific in the mailing
lists.

Also, for unsaturated carbons, the unsat option must be used. So, one
simply makes a new index file with two carbons atoms each on each side
of the unsaturated bond, correct?

Thank you for the help,

-Himanshu