What can I do with the Micelle Maker?
Micelle Maker creates models of micelles preferentially as a basis for molecular dynamics simulations using AMBER.
Which lipid types are available?
Currently we support all lipids that have been parameterized for AMBER, including those commonly used in experiments with membrane proteins, like DDM and SDS.
What is the distance betwen lipids?
The distance between lipids defines the distance between the lipid molecules used for the initial model building of the micelle. Inhouse validation has shown that stable micelles are obtained when using a distance between 3.0 - 4.0 Å
How do I know the number of lipids for my micelle of choice?
Please have a look at the help section, here we provide experimental data for micelles that can be built with the Micelle Maker. These information can guide you to build realistic micelle models.
How long does a job take?
Runtimes are between 2 and 20 minutes for the initial model building, 10 and 30 minutes including minimization, 30 and 60 minutes for a full equilibration (includes minimization) depending on the input parameters.
The micelle equilibration failed. What happened?
Micelle equilibration fails due to an unfavorable configuration of the initial micelle. Either you are just unlucky due to a "bad" random seed applied for building up the micelle, or your micelle parameters do not correspond to a feasible system. Please check your micelle parameters and try again.
How long is data stored on the web server?
Your results will be stored on the web server for 10 days.