normal calculating lipid order parameter.

  • scinikhil
  • scinikhil's Avatar Topic Author
  • Offline
  • Fresh Boarder
1 month 3 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

/ 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 (-:

GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru
Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl
Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov
Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

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 "./", line 149, in <module>
vector[j] = first[j] - second[j]
IndexError: list index out of range

Please Log in or Create an account to join the conversation.

1 month 3 weeks ago #8176 by riccardo
Replied by riccardo on topic calculating lipid order parameter.
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: ?

If so, then from here: I see that "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.

Please Log in or Create an account to join the conversation.

Time to create page: 0.092 seconds