Dear gmxers,
I am planning to analyze order parameter using g_order, but some problems
always puzzle me. For convenience, I describe the first problem as follows:
Assume that there are two polymer chains H-[CH2-CH(OH)]n-H, now I want to
calculate the order parameter of two carbon atoms in the monomer along the
z-direction, that is, the Sz=1.5*<cos(θ)^2>-0.5, where θ is the angle between
the z-axis of the simulation box and the vector from one carbon atom to another
carbon atom. I have read the manual, only to find it seems that g_order has
different aim designed for acyl chains with long carbon tails. In fact, I am
not sure how it works from the manual. I wonder if the g_order can also
calculate order parameters defined above for two polymer backbone atom. If it
can, how to do it? Please kindly give me some hints. Thanks a lot for any reply.
Yours sincerely,
Chaofu Wu, Dr.
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