Supporting Information
SLIM: An Improved Generalized Born Implicit
Membrane Model
Julia Setzler1, Carolin Seith1, Martin Brieg2, Wolfgang Wenzel1*
1
2
Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021
Karlsruhe, Germany
Steinbuch Centre for Computing (SCC), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021
Karlsruhe, Germany
Software







PBEQ Solver1,2
SIMONA3
Gromacs4
PyMol5
Xmgrace6
Qtiplot7
Gimp8
All figures were created with PyMol, Qtiplot, Xmgrace and Gimp.
PBEQ Solver Settings
! adjustable PBEQ parameters
Set
EpsR
=
2
! dielectric constant for the reference environment
set
EpsP
=
2
! dielectric constant for the protein interior
set
EpsW
=
80
! solvent dielectric constant
set
Conc
=
0
! salt concentration
set
Focus =
1
! to have a refined calculation focused on the site
using a finner grid
set
Dcelc =
1.0
! the grid spacing in the finite-difference
(centered on Xcen,Ycen,Zcen)
set
Dcelf =
0.25
! the grid spacing in the finite-difference
(centered on Xcen,Ycen,Zcen)
set
Ledge =
25
! distance between a protein atom and a grid
! LEdge*2 for coarse-gird calculations
and LEdge/2 for fine-grid calculations (see below)
set Options
=
watr 1.4 reentrant
! Let's use the molecular surface
! membrane stuff
set Tmemb
=
set Zmemb
=
30
0
! thickness of membrane (along Z)
! center of membrane (along Z)
1
set epsM
set Htmemb
set epsH
=
=
=
2
5
7
! membrane dielectric constant
! thickness of headgroup region
! membrane headgroup dielectric constant
Melittin
For the starting conformation similar to explicit molecular dynamics results,9 we observe in three out of
the 20 simulations excessive kinked helices with kink angles smaller than 60°. A snapshot of the normally
and excessive kinked Melittin conformation is shown in Figure S1. If the simulations are started with
Melittin oriented horizontally inside the membrane, four out of the 20 simulations show excessive kink
angles. Using the starting conformation perpendicular to the membrane interface, only normally kinked
conformations occurred during our simulations.
Figure S1. Example of a normally kinked Melittin conformation(A) and an excessively kinked
conformation (B) taken from simulations with a starting conformation similar to explicit molecular
dynamics results.9
SLIM Performance Comparison
The performance comparison between SIMONA with the SLIM model and CHARMM10 with the HDGB
model of Tanizaki and Feig11 was run on a single node of the BWunicluster at the Steinbuch Centre for
Computing with one Intel Xeon E5-2670 processor. Only one thread was used in both cases. The
remaining cores of the compute node were empty. GCC compiler suite version 4.8.2 was used to
compile SIMONA and CHARMM with architecture specific optimizations and instruction sets enabled in
both cases. The CHARMM input was prepared with CHARMM-GUI,12 whose default settings for the
HDGB/GBMV implicit membrane model of Tanizaki and Feig11 were kept for the simulation.
References
1. W. Im, D. Beglov, B. Roux, Comput. Phys. Commun., 1998, DOI:10.1016/S0010-4655(98)00016-2.
2. S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, W. Im, Nucleic Acids Res., 2008,
DOI:10.1093/nar/gkn314.
3. T. Strunk, M. Wolf, M. Brieg, K. Klenin, A. Biewer, F. Tristram, M. Ernst, P. J. Kleine, N. Heilmann, I.
Kondov, W. Wenzel, J. Comput. Chem., 2012, DOI:10.1002/jcc.23089.
4. B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, J. Chem. Theory Comput., 2008,
DOI:10.1021/ct700301q.
5. L. L. C. Schrödinger, in The PyMOL Molecular Graphics System, Version 1.3r1, 2010.
6. Grace Home, http://plasma-gate.weizmann.ac.il/Grace/, (accessed July 30, 2013).
7. QtiPlot, http://soft.proindependent.com/qtiplot.html, (accessed July 30, 2013).
8. GIMP - The GNU Image Manipulation Program, http://www.gimp.org/, (accessed July 30, 2013).
9. S. Bernèche, M. Nina, B. Roux, Biophys. J., 1998, DOI:10.1016/S0006-3495(98)77604-0.
2
10. B. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C.
Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek,
W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M.
Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J.
Comput. Chem., 2009, DOI:10.1002/jcc.21287.
11. S. Tanizaki, M. Feig, J. Chem. Phys., 2005, DOI:10.1063/1.1865992.
12. S. Jo, T. Kim, V. G. Iyer, W. Im, J. Comput. Chem., 2008, DOI:10.1002/jcc.20945.
3