Downloads
In 2005 we published a paper that deals with the transition of a bilayer into a vesicle. In this paper we also describe the spontaneous formation of a bilayer from a initial configuration with lipids distributed randomly. We have used similar types of bilayers in many other simulations, and are still using them today. On this download page you can find the coarse grained configuration files belonging to an equilibrated lipid bilayer (244 molecules) surrounded by 6471 water molecules. For the exact model we used, we refer the reader to the above mentioned paper.
The simulation configuration files are (see the Manual for help):
- The simulation input file: input.pif
- The system configuration file: sysIT0.pxf
- The topology file of the lipid: G4T4T4.ptf
- The topology file of the water: W.ptf
- The parameter file: parameters.ppf
- The positions/velocities of the lipids: G4T4T4IT0.pcf
- The positions/velocities of the water molecules: WIT0.pcf
This model uses the bond and angle harmonic potentials for the bonded interactions and the Lennard-Jones potential for the non-bonded interactions. No charges are present on the particles, so no electrostatic potential is required. Similarly, no dihedrals, improper torsion or Urey-Bradley terms are present, and are, therefore, excluded. The Berendsen temperature and pressure coupling is used to keep the system in the NVT-ensemble. See the Theory section for more details.
The PumMa program is not yet available for download. Currently we are working together in close collaboration with several groups, and adapt PumMa according to their findings. The code might be available for public download at some moment in the near future.