Membrane Simulations in GROMACS
Lipid bilayers and membrane proteins
Justin A. Lemkul
September 13, 2013
jalemkul@[Link]
Objectives
• Learn the fundamentals of
– Self-consistent force fields
– Membrane and membrane protein
simulations
• Perform common analysis routines for
lipids
References
Background Theory
• Kandt, C.L., Ash, W.L., and Tieleman, D.P. (2007)
Methods 41: 475-488.
• [Link]
• Relevant to today’s example
– Kandasamy, S.K. and Larson, R.G. (2006) Biophys. J. 90: 2326.
– Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) J. Comput.
Chem. 30: 1952.
References
Tutorial Exercise Theory
• Biomolecular force fields often built in
stages
– Proteins, nucleic acids, lipids, other stuff…
• Important to use self-consistent
parameters
– Nowadays most force fields include support
for all major macromolecule types
References
Tutorial Exercise Theory
• Lipid parameters (NOT exhaustive!)
– CHARMM36
• Klauda, J.B. et al. (2010) J. Phys. Chem. B 114: 7830.
• Pastor, R.W. and MacKerell Jr., A.D. (2011) J. Phys. Chem.
Lett. 2: 1526.
– OPLS-AA
• Ulmschneider, J.P. and Ulmschneider, M.B. (2009) J. Chem.
Theory Comput. 5: 1803.
– GROMOS96
• Kukol, A. (2009) J. Chem. Theory Comput. 5: 615.
– AMBER
• Siu, S.W.I. et al. (2008) J. Chem. Phys. 128: 125103.
Setup
Tutorial Exercise Run
Analyze
• Tutorial files provided
membrane_tutorial/conf Sample configurations
/data Sample data
/gromos53a6_lipid.ff Force field
/mdp Run parameters
/scripts Accessory scripts
/top Topologies
/tpr Run input files
• Protocol online
[Link]
Setup
Tutorial Exercise Run
Analyze
• Challenge #1: selecting a force field
• Challenge #2: building the starting
configuration
– InflateGRO
• Kandt, C.L. et al. (2007) Methods 41: 475.
• Schmidt, T.H. and Kandt, C.L. (2012) J. Chem. Inf.
Model. 52: 2657.
– g_membed
• Wolf, M.G. et al. (2010) J. Comput. Chem. 31:
2169.
Setup
Tutorial Exercise Run
Analyze
• Placing a protein: editconf –center
Protein COM coincident with Protein COM above
membrane COM membrane COM
Setup
Tutorial Exercise Run
Analyze
• Placing a protein: editconf –center
editconf –center x/2 y/2 z/2
–box x y z
Protein COM coincident with Protein COM above
membrane COM membrane COM
Setup
Tutorial Exercise Run
Analyze
• Placing a protein: editconf –center
g_traj –n [Link] –ox
–nox –noy –z –com
editconf –center x/2 y/2 z/2
–box x y z editconf –center x/2 y/2 z*
-box x y z
Protein COM coincident with Protein COM above
membrane COM membrane COM
Setup
Tutorial Exercise Run
Analyze
• Topology generation: different approaches
– With CHARMM, simply use pdb2gmx
• Check contents of [Link]
– With others, introduce lipid-specific terms
• [Link] (Berger parameters)
• Approach used here to combine Berger lipids with
GROMOS96
• More complicated procedure for combining all-
atom proteins with united-atom lipids
– [Link]
Setup
Tutorial Exercise Run
Analyze
[Link] [Link]
[ defaults ] [ defaults ]
[ atomtypes ] [ atomtypes ]
[ nonbond_params] [ nonbond_params]
Lipid-Lipid terms
Lipid-GROMOS terms
[ pairtypes ] [ pairtypes ]
[Link]
[ bondtypes ]
[ angletypes ]
[ dihedraltypes ] [ dihedraltypes ]
Setup
Tutorial Exercise Run
Analyze
• Membrane-specific run settings
– comm_grps
– tc_grps
– ref_t
• Run for tens or
hundreds of ns
Setup
Tutorial Exercise Run
Analyze
• Notes on cutoffs
– Berger: plain 1.0-nm cutoffs
– GROMOS96: 0.9/1.4-nm twin-range
• Here we use 1.2-nm (single-range)
– APL and membrane properties unaffected
– Peptide secondary structure
Setup
Tutorial Exercise Run
Analyze
• Analysis techniques to be covered
– Lateral diffusion/diffusion constant
– Membrane thickness
– Deuterium order parameters
– Area per lipid
Setup
Tutorial Exercise Run
Analyze
• Index groups
– Lateral diffusion: P8 atoms
– Membrane thickness: P8 atoms in each leaflet
– Deuterium order parameters: each acyl C
atom
Setup
Tutorial Exercise Run
Analyze
• All P8 atoms
– Use make_ndx or g_select
• In make_ndx: a P8
• In g_select: name P8;
• Top and bottom leaflet P8 atoms
– Use g_select (file p8_selection.dat)
top_p8 = name P8 and (z > 3.2);
bot_p8 = name P8 and (z < 3.2);
top_p8;
bot_p8; About middle of box
Setup
Tutorial Exercise Run
Analyze
• Acyl chain C atoms – use make_ndx
– sn-1 and sn-2 chains separately
a C34 a C15
a C36 a C17
a C37 a C18
… …
a C50 a C31
Setup
Tutorial Exercise Run
Analyze
• Lateral diffusion
echo 0 | g_msd –s [Link] –f [Link] –n all_p8.ndx –
lateral z –o msd_p8.xvg
– May have to deal with PBC separately for each
leaflet
• Membrane thickness
echo 0 1 | g_dist –s [Link] –f [Link] –n
top_bot_p8.ndx
– Only z-distance important (x/y should be ≈0)
– May not tell the whole story
Setup
Tutorial Exercise Run
Analyze
• Deuterium order parameters
g_order –s [Link] –f [Link] –n [Link] –od
deuter_sn1.xvg –d z
g_order –s [Link] –f [Link] –n [Link] –od
deuter_sn2.xvg –d z
– Important to consider equilibration time,
usually need –b
– Unsaturated lipids require –unsat option
• Run separately for double bond atoms
–Cn-1–Cn=Cn+1–Cn+2–
Setup
Tutorial Exercise Run
Analyze
• Area per lipid
– Trivial for pure membranes
(Box-X * Box-Y)/(# of lipids per leaflet)
– Use g_energy to extract Box-X and Box-Y
g_energy –f [Link] –o [Link]
perl scripts/[Link] [Link] 64
Setup
Tutorial Exercise Run
Analyze
• Area per lipid (and membrane thickness)
– Complicated problem if a protein is embedded
– Shameless self-promotion: GridMAT-MD
[Link]
Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) J. Comput. Chem. 30: 1952.