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

himanshu khandelia hkhandelia at gmail.com
Wed Jul 2 12:32:11 CEST 2008


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

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,


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