Dear Gromacs Users,
I have a question on how to use g_order to get the order parameters
correctly for an inverted hexagonal (HII) phase and compare it with
experimental values from NMR.
I read some articles, including following one:
Vermeer, Louic S., et al. "Acyl chain order parameter profiles in
phospholipid bilayers: computation from molecular dynamics simulations and
comparison with 2H NMR experiments." *European Biophysics Journal* 36.8
But, still, I am not quire sure if I understood it correctly.
*In NMR experiments*, there is a direction for the magnetic field which is
applied to the sample (say Z_exp). This Z_exp is less likely to be exatly
parallel to and will make an angle with the normal vector (n_exp) to the
bilayer, or to the cylindrical axis (C_exp) of HII phase in experiment. (I
simplified the situation, hope it does not affect the following argument)
*In our simulations 1) For bilayer case:*
Given a bilayer in XY plane, we calculate the order parameters values
regarding to the normal vector (n_sim) to the bilayer, i.e. the Z axis
How can we be sure this Z_sim is the same with Z_exp? If these two are not
close/same, comparison does not make too much sense. Does it?
*2) For HII phase case:*
Given a HII phase with cylinders parallel to the Z_sim axis, What is the
situation for calculating the order parameters? Shall we take Z_sim or the
radial vector? By radial vector, I mean the vector pointing to the cylinder
axis. This radial vector will be locally normal to the lipid cylinder at
each point? Seems like we are doing it like bilayer.
Here again, the problem with weather or not Z_sim=Z_exp exist.
Hopefully I could explain the problem clearly.
Thanks in advance for your comments.
*Rewards work better than punishment ...*
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