Supporting Information for:
On the Calculation of Acyl Chain Order Parameters
from Lipid Simulations
Thomas J. Piggot*, Jane R. Allison, Richard B. Sessions and Jonathan W. Essex
*Correspondence should be addressed to:
Thomas Piggot ([email protected] and [email protected])
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2 Figure S1 – Order parameters calculated for the OPLS-AA force field POPC simulation using the NMRlipids all-atom script (black) and the standard GROMACS g_order program (version 5.0.6) with the –unsat option for carbons 9 and 10 (blue). The results with the standard g_order program closely match those previously reported for this all-atom force field.
Figure S2 – Slipids POPC membrane properties using a 1.0 nm cut-off for the van der Waals interactions. Top Left: Area per lipid. Top Right: Electron density profile across the
membrane. Bottom Left: Deuterium order parameters compared to experiment (as also reported in the main text). Bottom Right: P-N head group angle probabilities.
0 20 40 60 80 100 Time (ns) 0.62 0.64 0.66 0.68 0.7
Area per Lipid (nm
2 )
-4 -2 0 2 4
Relative position from center (nm)
0 50 100 150 200 250 300 350 Electron density (e nm -3 ) POPC Water Phosphate Choline
Glycerol and Carbonyl
2 4 6 8 10 12 14 16 18 Carbon Number -0.04 0 0.04 0.08 0.12 0.16 0.2 0.24 0.28 -SCH sn-1 pro-S sn-1 pro-R Ferreira sn-1 sn-2 pro-S sn-2 pro-R Ferreira sn-2 pro-S Ferreira sn-2 pro-R 0 30 60 90 120 150 180 P-N Angle (degrees) 0 0.004 0.008 0.012 0.016 Probability Density
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4 Figure S3 – Order parameters calculated for the CHARMM36 force field POPC simulation using: the standard GROMACS g_order program (version 4.5.7) without the –unsat option (black), the tool used in our previous comparative force field study (orange), and the proposed fix of the g_order program provided by Christopher Neale (blue triangles).
Figure S4 – Order parameters calculated for the sn-1 (top) and sn-2 (bottom) chains of the CHARMM36 force field POPC simulation using the modification to the fixed version of g_order originally provided by Reid Van Lehn (see also Figure S5) so as to calculate the individual hydrogen atoms SCH. The results from the NMRlipids united-atom analysis approach are also shown for comparison.
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6 Figure S5 – Order parameters calculated for the CHARMM36 force field POPC simulation using the different applications of the fixed version of g_order provided by Reid Van Lehn. The original approach provided did not have a reverse order of the atoms for C10 in the required input dat file (see Appendix S1 later in this document for more information on use of this program) and therefore the calculation for this carbon was not correct (black line). Using the appropriate order of atoms in the dat file with the unmodified program resulted in incorrect order parameters (negative of the correct order parameter) due to a part of the code that was intended to check for incorrect reverse atom orders in the dat file (red line). Removal of this part of the code produces correct order parameters (green line).
Figure S6 – Order parameters calculated for the CHARMM36 force field POPC simulation using the approach of Gapsys et al. 1 manually implemented in the fixed version of g_order (see the main paper for more details). The NMRlipids united-atom approach using the GROMACS protonate program generates identical results for the unsaturated carbon atoms within the double bond (9 and 10), as does the g_lomepro program (when this program is used appropriately, again see the main paper for more information).
8 8 Simulation pro-R NMRlipids pro-S NMRlipids pro-R g_order pro-S g_order Kp3a -0.190 -0.167 -0.181 -0.173 Kp3b -0.177 -0.135 -0.168 -0.141 Kp4a -0.195 -0.159 -0.187 -0.164 Kp4b -0.179 -0.135 -0.170 -0.139 Optimal 1 -0.180 -0.123 -0.173 -0.128 Optimal 2 -0.180 -0.149 -0.173 -0.155
Table S1 – SCH splitting at C2 in the sn-2 chain for the GROMOS-CKP force field calculated from the POPC simulations performed in our previous comparative force field work 2, using both the NMRlipids analysis method and the modified version of g_order. The first 4 simulations refer to those as described in Table 1 of this previous work, while the final two simulations (Optimal 1 and 2) are those that were performed with optimal parameters (the results for Optimal 1 are also shown in the main paper of this current study). The first four rows in the table are for simulations started from a GROMOS 43A1-S3 POPC membrane structure. These, therefore, initially had an orientation of C2 that produces an incorrect splitting of the pro-R and pro-S SCH (see the main text for further details). The simulations in the final two rows of the table were started from a CHARMM27r POPC membrane structure and therefore initially had C2 structures closer to experiment (see Table 1 of Pastor et al. 3 for sn-2 C2 splitting with different CHARMM lipid force fields). These simulations were all performed for 200 ns with the SCH analysis performed on the complete simulations. Simulations Kp3a and Kp3b used PME for the long-range electrostatic interactions while simulations Kp4a, Kp4b, Optimal 1 and Optimal 2 used a reaction-field approach.
Simulation pro-R NMRlipids pro-S NMRlipids pro-R g_order pro-S g_order Lp1a -0.151 -0.131 -0.144 -0.136 Lp1b -0.164 -0.134 -0.157 -0.138 Lp2a -0.168 -0.144 -0.161 -0.148 Lp2b -0.169 -0.162 -0.162 -0.165 Optimal 1 -0.158 -0.144 -0.152 -0.148 Optimal 2 -0.167 -0.130 -0.161 -0.134
Table S2 – SCH splitting at C2 in the sn-2 chain for the GROMOS 53A6L force field calculated from the POPC simulations performed in our previous comparative force field work 2, using both the NMRlipids analysis method and the modified version of g_order. The first 4 simulations refer to those as described in Table 1 of this previous work, while the final two simulations (Optimal 1 and 2) are those that were performed with optimal parameters (the results for Optimal 1 are also shown in the main paper of this current study). The first four rows in the table are for simulations started from a downloaded GROMOS 53A6L POPC membrane structure. The simulations in the final two rows of the table were started from a CHARMM27r POPC membrane structure and therefore initially had C2 structures closer to experiment (see Table 1 of Pastor et al. 3 for sn-2 C2 splitting with different CHARMM lipid force fields). These simulations were all performed for 200 ns with the SCH analysis
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10 Appendix S1 – Installation and Usage of the Modified g_order Program
As discussed within the main text, a modified GROMACS program g_order has been included within the supporting information of this work so as to help enable accurate and rapid calculation of SCH in united-atom systems. As also discussed, the majority of the modifications to this program were performed by Reid Van Lehn, with some relatively small modifications and additions in this work. These additions were included to: correct the calculation of the unsaturated SCH, calculate the individual order parameters of the hydrogen atoms in united-atom methylene groups, and change some of the default behaviour of the program including the outputting of results. Because of this we therefore ask that if you use this code you not only appropriately cite the GROMACS code and the methodology used within this approach (e.g. 4) but you also reference the work of Van Lehn and Alexander-Katz 5. The program also retains the modifications reported within that work to calculate radial order parameters at defined distances from a reference group. These options have not been tested in this work and questions regarding these calculations should be directed to those authors.
Below are some instructions for the installation and usage of this modified GROMACS program:
1. Download and unpack the GROMACS 4.6.7 source code from the GROMACS website. 2. Move the rvl_tjp_bilayer_order_467.c file of this supporting information into the gromacs-4.6.7/src/tools/ directory of this downloaded source code, replacing the normal version of g_order.c. For example:
“cp rvl_tjp_bilayer_order_467.c gromacs-4.6.7/src/tools/g_order.c”
3. Install this now modified version of GROMACS. Something along the lines of:
“cmake ../ DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6.7_fix_op
-DGMX_BINARY_SUFFIX=_4.6.7_fix_op -DGMX_DEFAULT_SUFFIX=OFF && make -j 8 && sudo make install”
4. Check that the command “/usr/local/gromacs-4.6.7_fix_op/bin/g_order_4.6.7_fix_op –h” (but here obviously using the location of wherever you installed this version of GROMACS and the correct name of the modified g_order program, as determined by the cmake options you used in 3.) now shows a program which has an -li option for an input dat file. If so, the modified version should be installed.
5. If your simulation was performed with a more recent version of GROMACS than version 4.6.7, you need to remake a 4.6.7 version of your system tpr. This should be easy by simply re-running grompp with your newly installed GROMACS 4.6.7 (you may need to change some mdp options here and/or use the -maxwarn option of grompp, but what you have doesn't matter as the tpr will only be used to run the newly modified version of g_order). 6. Run the modified g_order program using your newly created 4.6.7 tpr for the -s option, your simulation xtc for -f, and an appropriate dat file for the -li option depending upon the united-atom force field used. Six dat files for each of the united-atom POPC force fields studied in this work (Berger, CHARMM36-UA, GROMOS43A1-S3, GROMOS53A6L,
GROMOS-CKP and OPLS-UA) are also including as part of this supporting information. 7. Select the membrane when prompted to do so.
8. The order parameters will be output to the files specified by the -od1 and -od2 options for the sn-1 and sn-2 tails respectively (as labeled in the dat file). The order parameters are reported individually for both hydrogen atoms in saturated methylene groups. For ease of plotting with xmgrace, values for any methine hydrogen atoms are copied into both of the columns in the output files.
Finally, if you wish to try out the manual implementation of the measured CHARMM36 all-atom angles for the double bond you simply need to replace UNSAT with UNSAT_AA in the dat file. With this option, it is possible to produce quite accurate order parameters for the all-atom force fields tested in this work. However, we recommend that an all-all-atom tool be used instead for this purpose.
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12 Supporting References
(1) Gapsys, V.; de Groot, B. L.; Briones, R., Computational Analysis of Local Membrane Properties. J. Comput. Aided Mol. Des. 2013, 27 (10), 845-858.
(2) Piggot, T. J.; Piñeiro, Á.; Khalid, S., Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. J. Chem. Theory Comput. 2012, 8 (11), 4593-4609.
(3) Pastor, R. W.; MacKerell, A. D., Development of the CHARMM Force Field for Lipids. J. Phys. Chem. Lett. 2011, 2 (13), 1526-1532.
(4) Douliez, J.-P.; Ferrarini, A.; Dufourc, E.-J., On the Relationship Between C-C and C-D Order Parameters and its use for Studying the Conformation of Lipid Acyl Chains in Biomembranes. J. Chem. Phys. 1998, 109 (6), 2513-2518.
(5) Van Lehn, R. C.; Alexander-Katz, A., Membrane-Embedded Nanoparticles Induce Lipid Rearrangements Similar to Those Exhibited by Biological Membrane Proteins. J. Phys. Chem. B 2014, 118 (44), 12586-12598.
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