unanswered Order parameters calculation

  • saeedimasine
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6 years 5 months ago #7410 by saeedimasine
Order parameters calculation was created by saeedimasine
Hi,
I used do-order-gmx5.py for order parameter calculation of my simulated system which was prepared by CHARMM-GUI server and consists of 70 POPC, 70 POPE and 60 CHOL molecules in martini force field, I got the following error, I tried to know the code but I didnt know how to change it to work for my system. If you have any idea about this error, please let me know,

Thanks in advance,

./do-order-gmx5.py traj.xtc topol.tpr 5000 10000 5 0 0 1 70 POPC
(Normalized) orientation of bilayer normal: ( 0.000 | 0.000 | 1.000 ).

Frame NC3-PO4 PO4-GL1 GL1-GL2 GL1-C1B GL2-C1A C1A-D2A D2A-C3A C3A-C4A C1B-D2B D2B-C3B C3B-C4B
Output all coordinate files
:-) GROMACS - gmx trjconv, VERSION 5.1.2 (-:
.....
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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