8.1 Running a Membrane Algorithm

Running a membrane algorithm will build the lipid layers of your membrane according your scheme or manipulate existing membranes.

Your scheme gets presented by the sample lipids that you've set up.

When generate the bilayer?

You can start the calculation as soon as

However, the best time to generate the layers is just before you finish your membrane, ensuring that they are up to date.

Running an algorithm

To start, press the button in the Membrane View. A dialog will appear which enables you to choose between the available algorithms.

The dialog will display information which is available from the selected algorithm.

The dialog here displays information about the algorithms that are available. One important thing is the support of microdomains If an algorithm does not support them, note that all microdomains in the membrane will be ignored by using only the lipids of the default area.

Another flag indicates if lipids which are already in the membrane have to be overridden. If so, all lipids will be removed first, otherwise this choice is up to you. 

In the lower right corner you'll find two additional options:

Show Protocol

Displays a protocol just after the algorithm has terminated which contains information about the last run

The message window contains an option to export the runtime graph of the algorithm in Grace .xvg format. This graph can be used for publishing or comparing issues.

Unique Random

Here you can define a seed for the random instance of the algorithm. This seed will be used by the random instance to produce its outcome. Using the same seed on a same initial state of a membrane leads to an exact same result. This feature can be used in order to reproduce a result or to see how eventual changes of settings take effect, compared to a previous run. Disabling this feature will lead to a non-deterministic behavior.

Press 'Start' after you've made your decision to commence the selected algorithm.

It will either start immediately or show its settings dialog first, if the algorithm provides one.

A membrane algorithm, at halftime

You can request an algorithm to stop at any time by pressing the 'Stop' button. The algorithm will not break immediately, but terminate the next best moment, marking the bilayer as completed.
It is up to you if you're satisfied with the result or if you want to restart.

The Random Algorithm even requires you to stop it manually, since its runtime is infinite.

While running an algorithm, you can switch off its real time visualization and minimize the MembraneEditor into the system-tray of your OS. This will decrease CPU costs what makes your algorithm go a little faster. Press  for this function. 

You may disable the statistics for the same purpose by pressing .

Some algorithms may even be controlled while they are running. For that they provide a control panel that will appear when you start. Use 

the button in order to show/hide the runtime controls.

Rerunning algorithms

When you rebuild your layers, you will have to decide what to do with the existing lipids. Some algorithms allow you to maintain them while others request you to remove them first. However, you can remove lipids by using either the 'Clear All' or the more specific 'Clear Lipids'
options in the upper toolbar.

You can also use the fact that lipids can be kept in order to mix algorithms. Here are 2 examples:

A membrane generated with a random algorithm embedded in a microdomain that has been generated before by the linear algorithm.

This membrane has been refined by the "Simulated Annealing" algorithm after a random algorithm has built the initial lipid set-up.