[gmx-users] Order parameter calculation

[Sheikh Imamul Hossain]

Hi all,
I am trying to calculate order parameter for DPPC monolayer using
do-order-milti.py script.Actually, the monolayer consists of 716 CG DPPC
and 307 CG POPG lipid molecules. The system consists two such monolayer
separated by a water slab. I run the simulation for 3 microsecond and
renamed the trajectory file as traj.xtc to  use the command
 ./do-order.py traj.xtc 0 3000000 20 0 1 0 716 DPPC
I got following output
(Normalized) orientation of bilayer normal: ( 0.000 | 1.000 | 0.000 ).

   Frame NC3-PO4 PO4-GL1 GL1-GL2 GL1-C1A GL2-C1B C1A-C2A C2A-C3A C3A-C4A
C1B-C2B C2B-C3B C3B-C4B
 -----------------------------------------------------------------------------------------------
Output all coordinate files
echo DPPC | trjconv -f md.xtc -b 2000000 -e 3000000 -sep -skip 5 -pbc whole
-o frame_dump_.gro > /dev/null
/bin/sh: 1: trjconv: not found
Starting P2 calculation
-----------------------------------------------------------------------------------------------
Snapshots analysis done.

Computing averages...

          NC3-PO4 PO4-GL1 GL1-GL2 GL1-C1A GL2-C1B C1A-C2A C2A-C3A C3A-C4A
C1B-C2B C2B-C3B C3B-C4B
-----------------------------------------------------------------------------------------------
 average
 -----------------------------------------------------------------------------------------------
Abs average order parameters for carbon chains <Sn> =    0.000
Results written in "order.dat".
The order.dat gives same result "Abs average order parameters for carbon
chains <Sn> =    0.000 "

How can I solve this problem to calculate the order parameters for DPPC and
POPG lipids.

Regards
Imamul
PhD Research Student