(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.
- 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). - 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:Following set of topologies contains mistakes (!!!). We are analysing and rebuilding them now.
- Ready bilayers for molecular dynamics.
[..coming soon..] - 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.
doi:10.1134/S1990747812050145 - 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
- 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.