normal Order Parameter Calculation

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6 years 8 months ago #7329 by Imamul
Order Parameter Calculation was created by Imamul
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

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6 years 8 months ago #7330 by peterkroon
Replied by peterkroon on topic Order Parameter Calculation
Where did you get the script? It looks like it's a version meant for Gromacs 4 --- note the call to `trjconv` instead of `gmx trjconv`. You can try to find a new one, or fix it yourself.

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6 years 8 months ago #7331 by Imamul
Replied by Imamul on topic Order Parameter Calculation
Hi Peterkroon,
Thanks for your reply. I already edited the script trjconv to gmx trjconv and made a copy of my tpr file and named it as topol.tpr. Now everything looks fine.
Regards
Imamul

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6 years 8 months ago #7332 by Imamul
Replied by Imamul on topic Order Parameter Calculation
Hi all,
I got the average order parameters for carbon chains <Sn>=0.417 for DPPC by using the command
For Sx calculation "./do-order.py md_traj.xtc 2900000 3000000 5 1 0 0 1432 DPPC"
For Sy calculation "./do-order.py md_traj.xtc 2900000 3000000 5 0 1 0 1432 DPPC"
Scd=(2/3)Sx+(1/3)Sy=0.417
Most of the papers reported that the DPPC carbon chains order parameter value nearly between 0.10~0.25.
I am failed to find out my problem. Though the area per lipid has matched with the published results.
I am wondering whether my obtained result and calculation method are correct or not.
Regards
Imamul

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6 years 8 months ago #7333 by p278107
Replied by p278107 on topic Order Parameter Calculation
Hi,
Maybe the reference DPPC order parameter you got is from all atomistic simulation. The way of order parameter computation is different for all atomistic and coarse-grain. There is no point to compare them.
regards,
liuyang

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6 years 8 months ago #7334 by jbarnoud
Replied by jbarnoud on topic Order Parameter Calculation
Hi,

I find your refeence order parameter rather low. Baoukina et al. reported order parameters closer to your 0.4 for a liquid extended phase: < pubs.acs.org/doi/full/10.1021/la702286h > figure 4A.

As Liuyang remarked, your reference may be from atomistic simulations.

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4 years 4 months ago - 4 years 4 months ago #8335 by cm
Replied by cm on topic Order Parameter Calculation
i am also trying to do order parameter calculation but i am getting this error
./do-order-gmx5.py traj.xtc topol.tpr 0 100000 20 0 1 0 6552 POPC
g P2 calculationTaking care of snapshot frame_dump_0.gro
Traceback (most recent call last):
File "./do-order-gmx5.py", line 149, in ?
vector[j] = first[j] - second[j]
IndexError: list index out of range
Last edit: 4 years 4 months ago by cm.

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2 years 11 months ago #8929 by sajjad
Replied by sajjad on topic Order Parameter Calculation
Do you solve this problem to calculate the order parameters for DPPC and POPG lipids. I am also face such type of problem. if you solve pleas tell me.

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