[gmx-users] g_order

[shahab shariati]

Dear gromacs users

My system contains DOPC + cholesterol + drug + water molecules.

For obtaining deuterium order parameter for the DOPC acyl
chains, first, I prepared sn1 and sn2.ndx files. Then I used

g_order -s md.tpr -f md.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order.xvg

g_order -s md.tpr -f md.xtc -n sn2.ndx -d z -od deuter_sn2.xvg -o order.xvg


when I open deuter_sn1.xvg, deuter_sn2.xvg and order.xvg files, these files
are empty as follows:
----------------------------------------------------------------------------------------
# This file was created Sat Dec 21 15:26:16 2013
# by the following command:
# g_order -s md.tpr -f md.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o
order.xvg
#
# g_order is part of G R O M A C S:
#
# Getting the Right Output Means no Artefacts in Calculating Stuff
#
@    title "Deuterium order parameters"
@    xaxis  label "Atom"
@    yaxis  label "Scd"
@TYPE xy



------------------------------------------------------------------------------------------

# This file was created Sat Dec 21 15:28:23 2013
# by the following command:
# g_order -s md.tpr -f md.xtc -n sn2.ndx -d z -od deuter_sn2.xvg -o
order.xvg
#
# g_order is part of G R O M A C S:
#
# Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
#
@    title "Order tensor diagonal elements"
@    xaxis  label "Atom"
@    yaxis  label "S"
@TYPE xy



-----------------------------------------------------------------------------------------

What is the reason of this issue?

How to resolve that?

What is difference between "Scd" and "S"?

Any help will highly appreciated.