(ATTENTION! MATERIAL UPDATED!) For lipid bilayer modelling the whole toolchain was built: from creating membranes to MD trajectory analysis. We use OPLS-AA forcefield with Berger potentials for alcane dihedrals integrated.

  1. Addings to OPLS-AA Forcefield.
    We use OPLS-AA with some includings; «includings» are overlays on the standart GROMACS forcefield files. Patch for GROMACS OPLS-AA forcefield  is here: lipid-patch-opls. Please unpack it into /usr/share/gromacs/top (for gmx 4.0.*) or into /usr/share/gromacs/top/oplsaa.ff/ (for gmx >4.5).
  2. Lipid topologies
    We can prepare any other lipid topology with our developed topology-preparator. We note that topology works imporperly without OPLS patch (see above).
    Rebuild topolgies have modifications in OPLS patch are here: 

    1. POPC

    Following set of topologies contains mistakes (!!!). We are analysing and rebuilding them now.

    1. DPPC
    2. DPPS
    3. Cholesterol
    4. POPE
    5. DOPE
    6. POPS
    7. dops
    8. dmps
  3. Ready bilayers for molecular dynamics.
    [..coming soon..]
  4. Citation:

    • Nesterenko, A. M., & Ermakov, Y. a. (2013). Molecular-dynamic simulation of phospholipid bilayers: Ion distribution at the surface of neutral and charged bilayer in the liquid crystalline state. Biochemistry (Moscow) Supplement Series A: Membrane and Cell Biology, 6(4), 320–328.
    • Marukovich, N., McMurray, M., Finogenova, O., Nesterenko, A., Batischev, O., & Ermakov, Y. (2013). Interaction of Polylysines with the Surface of Lipid Membranes: The Electrostatic and Structural Aspects. Advances in Planar Lipid Bilayers and Liposomes, 17(29), 139–166. doi:10.1016/B978-0-12-411516-3.00006-1