GROMACS tools for analyzing membrane trajectories

Membrane undulation spectrum

I wrote a gromacs 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.

I used the code to analyze simulations in my first fullerene paper, ref. [1] above; so if you use the tool, please to cite that paper.
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!
aggregation.png

Aggregation

g_aggregate.zip: click here to download.

If you use this tool, please cite:
Lipid Membranes as Solvents for Carbon Nanoparticles. J. Barnoud, G. Rossi, L. Monticelli, Phys. Rev Letters, (2014), 112, 068102
27_grid_thickness.png

Membrane thickness

g_thickness.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.
27_grid_density.png

Membrane density

g_mydensity.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.
27_grid_order.png

Membrane ordering

g_ordercg.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.

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.