This algorithm combines two useful features: The first feature is that you are able to define the number of lipids on each side. You can do this by either entering a total count or by defining a floating number of area per lipid in Angstrom2.
The second feature is that all lipids will be evenly distributed as well as possible. This is very useful for refining existing membranes or for creating membranes with exact numbers and enough room left, e.g. for various simulations.
For example, high density algorithms like the Advanced Random Placing in Superb mode can be used to generate membranes with very densely packed lipids. These algorithms may also be needed if the used lipid model has a very space consuming conformation. After the membrane is generated, the Distributor algorithm can be used to achieve a user-defined number of lipids on each side (e.g. equally distributed on each side).
The controls can be accessed during runtime. They will let you enter your desired amounts for each membrane side differently. To apply the counts, wait for the Apply Counts button to activate after your submission. You can also Pause the algorithm to have a better look at the state.
The algorithm automatically terminates if the defined values are achieved. By deactivating the checkbox AutoStop, the algorithm will run until the user terminates it by pressing Stop.
- Written by bjoern
- Category: Cm2help 8. The Lipid Bilayer
- Published: 14 September 2013
- Hits: 2140