Fullerene structures and topologies

C60_and_F16.jpg

Atomistic simulations

C60 fullerene topology
C60 fullerene structure (single molecule)

MARTINI CG simulations

F16 fullerene topology
MARTINI force field file with bead types for CNP, PEG and PS
F16 fullerene structure (single molecule)
F16 fullerene in octane: structure, topology, solvent force field file, mdp file.

If you use this material, please cite:

[1] A simulation study of fullerene translocation through lipid membranes. J. Wong-ekkabut, S. Baoukina, W. Triampo, I-M.Tang, D. P. Tieleman, L. Monticelli. Nature Nanotechnology (2008), 3, 363-368

and:

[2] On atomistic and coarse-grained models for C60 fullerene. L. Monticelli, J. Chem. Theory Comput. (2012), 8, 1370−1378 (DOI: 10.1021/ct3000102).

Martini polymers: PEG and polystyrene (PS)

Self-assembly of β-OG–C12E2–water mixtures

Topologies

Topology for PS-100 (A mapping):
PS100_Amap.itp

Topology for PEG-100:
PEG100.itp

Topology for non-ionic surfactants, CiEj:
C12E2.itp
C12E4.itp
C12E6.itp

Topology for β-octylglucopyranoside:
betaog.itp

Martini v2.1 itp force field file (including all interactions for carbon nanoparticles and polymers):
martini_v2.1_CNP_PEG_PS.itp

Structure files

PS100 in benzene:
PS100_in_BENZ2652.gro , PS100_Amap_benz.top

Small lamellar patch of C12E2 in water:
216xC12E2_water_lamellar.gro , 216xC12E2_water_lamellar_top.top

PEG-100 chain in water:
PEG100_water.gro , PEG100_water_top.top

If using our polystyrene topologies, please cite:

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case. G. Rossi, L. Monticelli, S. R. Puisto, I. Vattulainen, T. Ala-Nissila.
Soft Matter (2011), 7, 698-708

If using our PEG topologies, please cite:

A Coarse-Grained MARTINI Model of Polyethylene Glycol and of Polyoxyethylene Alkyl Ether Surfactants, G. Rossi, P.F.J. Fuchs, J. Barnoud, and L. Monticelli, J. Phys. Chem. B, DOI:10.1021/jp3095165 (in press)

GROMACS tools for analyzing membrane trajectories

Membrane undulation spectrum

Tool to calculate the undulation spectrum from bilayer simulations. For the theory, I referred to the following papers:

  • Elastic properties of lipid bilayers: theory and possible experiments. W. Helfrich, Zeitschrift fur Naturforschung, 28(11), 693-703 (1973)
  • Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Lindahl, E. & Edholm, O. Biophys. J. 79, 426-433 (2000).
  • Effect of undulations on surface tension in simulated bilayers. Marrink, S.J. & Mark, A.E. J. Phys. Chem. B 105, 6122-6127 (2001).

g_und.c: click here to download
The code was used in my first fullerene paper, ref. [1] above; so if you like that, you are welcome to cite it. The code works with topologies from gromacs 3.x, so if you are using gromacs 4.x you can (a) adapt the code or (b) make a topology for gromacs 3. Please do let me know if you find mistakes in the code!

27_grid_thickness.png

Membrane thickness

g_thickness.tar.gz: click here to download
If you use this tool, please cite:

Free Energy of WALP23 Dimer Association in DMPC, DPPC, and DOPC bilayers
N. Castillo, L. Monticelli, Jonathan Barnoud, and D.P. Tieleman
Chem. Phys. Lipids (2013), 169, 95-105.

27_grid_density.png

Membrane density

g_mydensity.tar.gz: click here to download
If you use this tool, please cite:

Free Energy of WALP23 Dimer Association in DMPC, DPPC, and DOPC bilayers
N. Castillo, L. Monticelli, Jonathan Barnoud, and D.P. Tieleman
Chem. Phys. Lipids (2013), 169, 95-105.

27_grid_order.png

Membrane ordering

g_ordercg.tar.gz: click here to download
If you use this tool, please cite:

Free Energy of WALP23 Dimer Association in DMPC, DPPC, and DOPC bilayers
N. Castillo, L. Monticelli, Jonathan Barnoud, and D.P. Tieleman
Chem. Phys. Lipids (2013), 169, 95-105.

To make figures like the ones above

dispgrid.zip: click here to download
If you use this tool, please cite:

Free Energy of WALP23 Dimer Association in DMPC, DPPC, and DOPC bilayers
N. Castillo, L. Monticelli, Jonathan Barnoud, and D.P. Tieleman
Chem. Phys. Lipids (2013), 169, 95-105.

Berger lipids:
topologies adapted for use with the OPLS-AA force field

For mixing Berger UA lipids with OPLS-AA stuff, please refer to:

Membrane protein simulations with a united atom lipid and all-atom protein model: side chain transfer free energies and model proteins. D. P. Tieleman, J. L. MacCallum, W. L. Ash, C. Kandt, Z. Xu, L. Monticelli. J. Phys-Condens. Mat. (2006), 18, S1221-S1234.

lipid_se_OPLSAA_Berger_corrected.itp

DLPC.itp
DMPC.itp
DPPC.itp
POPC.itp
DOPC.itp
POPS.itp
POPE.itp