Our task is to numerically invetigate cellular bilayer membrane. In order to numerically simulate behavior of biological complex membrane, we need to have initially constructed membrane. However, building of complex membrane models is no simple task and requires tested algorithms. Molecular dynamics simulations on simple mixtures (less than 3-4 lipids) can be performed using a self-assembly approach, however generation of initial state of bigger membrane requires large computational cost.
So we are looking for most suitable free software tool to generate pre-built biological bilayer membranes, which will be used in further numerical investigation by Molecular Dynamics.
Thank you very much in advance,
Algis
Dear Algis,
Packmol is a free software for building initial configurations for Molecular Dynamics Simulations and makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.
http://m3g.iqm.unicamp.br/packmol/userguide.shtml
I hope you found this useful.
Seyedeh Tahereh Hosseini , Thank you very much. We will study Packmol.
All the best,
Hi,
CHARMM-GUI ( http://charmm-gui.org/?doc=input/membrane.bilayer ) might be suited for you. It allows you to build different membrane types (mono- and bilayers, nanodisks, micelles, etc.) using a wide range of different lipids. It can also generate the input files for many of the commonly used MD software.
- Badges
- Science topic