[gmx-users] a question on order parameter
leehk at umich.edu
Tue Sep 14 23:39:18 CEST 2004
Dear gromacs users,
I have used g_order and have some questions on results from g_order. In
my monolayer system, the interface between water and lipids are normal
to Z-axis, and lipids have CH2 tail regions. I wanted to know order
parameter (Scc) of acyl chains of lipids.
1) I expected to see symmetry of Sx and Sy, but Sy and Sz are
symmetrical, and Sx looks so different from Sy and Sz. could you
explain why it happens? Why Sy and Sz are symmetrical and Sx looks
2) I wanted to know order parameter of acyl chains of lipids in terms
of Z-axis. I did like below.
g_order -f ***.xtc -n ***.ndx -s ***.tpr -o ***.xvg -d z
And then, I read Z values for order parameter (Scc) of acyl chains of
lipids. Is that right way?
Thanks for help in advance.
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