Documentation
Below you can find the repository of the most commonly used parameters (and their descriptions)
in MOSAICS. Note, that not all options are necessary to perform a calculation (simulation) with MOSAICS.
Some examples and tutorials
on this website use the minimal number of options necessary for a given
application. Therefore, it is recommended to study those applications in combination with the brief
description of different options here.
Each parameter can be defined by using the syntax, \parameter{x}, where x
the value chosen for the parameter. In the below descriptions \parameter{a} indicates that
parameter has the default value a, otherwise parameter is listed as \parameter{ }.
In each case the argument type is explained.
To specify parameter options for performing a computation of a
given system with MOSAICS one has to define sets of parameters:
Defines parameters that are independent of the given system of interest. For example, performing
parallel tempering Monte Carlo can be done for any system and the implementation of the parallel
tempering MCMC is independent of the choice of the system.
These parameters define the model representation, which includes the resolution
(e.g. one center per nucleotide or atomistic), and the corresponding interaction
potential (e.g. physics based or statistical) describing how atoms (or centers) interact.
In the beginning of the .pdb files some parameters may be included to indicate
how to treat different chains.
This is used for hierarchical sampling and describe/specify how
regions and the elements in the region move in a Monte Carlo simulation.
Simulation parameters
To view this set of parameters click on
simulation parameters.
System parameters
To view these parameters click on
system parameters.
Header parameters
To view these parameters click on
header parameters.
Region parameters
To view these parameters click on
region parameters.