[gmx-users] Order Parameter for HII phase

[Mohsen Ramezanpour]

Dear Gromacs users,

I am interested in calculation of order parameter of lipids in a HII phase.

I am not sure about the correct command to use. Which one of the following
should I use to be able to compare my data with deutirated NMR experiments?

1) gmx order  -f  md.xtc  -n  index.ndx  -s  md.tpr  -o  order.xvg  -od
deuter.xvg  -d z  -szonly

or

2) gmx order  -f  md.xtc  -n  index.ndx  -s  md.tpr  -o  order.xvg  -od
deuter.xvg  -d z
(In this case, there are four columns of data (x, y, z for each carbon
atom).
The column 3 seems to be the same with when we include -szonly)

or anything else?

Corresponding available experimental data, I assume the second command
should be correct in my case . However, I am not sure x or y or what to use
for judging.

Cylinders in HII phase are parallel to the Z axis in my system.

Many thanks in advance for your comments
Mohsen
-- 
*Rewards work better than punishment ...*