Membrane Simulations in GROMACS

Lipid bilayers and membrane proteins

Justin A. Lemkul
September 13, 2013

[email protected]
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.

•  http://lipidbook.bioch.ox.ac.uk/

•  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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
 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 p8.ndx –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 lipid.rtp
– With others, introduce lipid-specific terms
•  lipid.itp (Berger parameters)
•  Approach used here to combine Berger lipids with
GROMOS96
•  More complicated procedure for combining all-
atom proteins with united-atom lipids
–  http://www.pomeslab.com/files/lipidCombinationRules.pdf
 Setup
Tutorial Exercise Run
Analyze

ffnonbonded.itp lipid.itp
[ defaults ] [ defaults ]
[ atomtypes ] [ atomtypes ]

[ nonbond_params] [ nonbond_params]
Lipid-Lipid terms
Lipid-GROMOS terms

[ pairtypes ] [ pairtypes ]

ffbonded.itp
[ 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 md.tpr –f traj.xtc –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 md.tpr –f traj.xtc –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 md.tpr –f traj.xtc –n sn1.ndx –od
deuter_sn1.xvg –d z
g_order –s md.tpr –f traj.xtc –n sn2.ndx –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 ener.edr –o box.xvg

perl scripts/area.pl box.xvg 64

 Setup
Tutorial Exercise Run
Analyze

•  Area per lipid (and membrane thickness)

– Complicated problem if a protein is embedded
– Shameless self-promotion: GridMAT-MD
http://www.bevanlab.biochem.vt.edu/GridMAT-MD/

Allen, W.J., Lemkul, J.A., and Bevan, D.R. (2009) J. Comput. Chem. 30: 1952.