normal calculating lipid order parameter.

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5 months 2 weeks ago #8175 by scinikhil
calculating lipid order parameter. was created by scinikhil
Hi all,

I'm new to CGMD, I have completed the simulation and would like to asses the lipid order parameter. I have used the following command

/do-order-gmx5.py newpbc.xtc step7_production.tpr 0 9973 1000 0 0 1
188 POPC

I have a total of 9973 frames and skipped in 1000. there is 188 POPC membrane. I ended up with the following error.

(Normalized) orientation of bilayer normal: ( 0.000 | 0.000 | 1.000 ).

Frame NC3-PO4 PO4-GL1 GL1-GL2 GL1-C1B GL2-C1A C1A-C2A C2A-C3A C3A-C4A C1B-D2B D2B-C3B C3B-C4B
Output all coordinate files
echo POPC | gmx trjconv -f newpbc.xtc -s step7_production.tpr -b 0 -e 9973 -sep -skip 1000 -pbc whole -o frame_dump_.gro > /dev/null
:-) GROMACS - gmx trjconv, 2018.2 (-:

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GROMACS: gmx trjconv, version 2018.2
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /media/data2/AQP$+abeta/monomer-CG-aqp/charmm-gui-156076644304/gromacs/order
Command line:
gmx trjconv -f newpbc.xtc -s step7_production.tpr -b 0 -e 9973 -sep -skip 1000 -pbc whole -o frame_dump_.gro

Will write gro: Coordinate file in Gromos-87 format
Reading file step7_production.tpr, VERSION 2018.2 (single precision)
Reading file step7_production.tpr, VERSION 2018.2 (single precision)
Group 0 ( System) has 28454 elements
Group 1 ( Protein) has 2364 elements
Group 2 ( Protein-H) has 2364 elements
Group 3 ( C-alpha) has 0 elements
Group 4 ( Backbone) has 0 elements
Group 5 ( MainChain) has 0 elements
Group 6 ( MainChain+Cb) has 0 elements
Group 7 ( MainChain+H) has 0 elements
Group 8 ( SideChain) has 2364 elements
Group 9 ( SideChain-H) has 2364 elements
Group 10 ( Prot-Masses) has 2364 elements
Group 11 ( non-Protein) has 26090 elements
Group 12 ( Other) has 26090 elements
Group 13 ( POPC) has 2256 elements
Group 14 ( PW) has 23655 elements
Group 15 ( ION) has 179 elements
Reading frame 0 time 0.000
Precision of newpbc.xtc is 0.01 (nm)
Using output precision of 0.001 (nm)
Reading frame 90 time 9000.000


GROMACS reminds you: "Wedged as we are between two eternities of idleness, there is no excuse for being idle now" (Anthony Burgess)

Starting P2 calculationTaking care of snapshot frame_dump_0.gro
Traceback (most recent call last):
File "./do-order-gmx5.py", line 149, in <module>
vector[j] = first[j] - second[j]
IndexError: list index out of range

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5 months 2 weeks ago #8176 by riccardo
Replied by riccardo on topic calculating lipid order parameter.
Hi,
I'm not the lipid expert here (I think I never used the script) but could you successfully compute the lipid order parameters in the GMX5 lipid tutorial: cgmartini.nl/index.php/tutorials-general...mx5#Order-parameters ?

If so, then from here: cgmartini.nl/index.php/tools2/other-tools I see that do-order-gmx5.py "has not been tested on many different simulations and might need manual editing.". So perhaps you need to adapt the script slightly to your (lipid) needs? Please have a look and post back here. Maybe in the meantime some lipid expert can even recognize already what the error you get is about.

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