Molecular Dynamics Integrators#
Molecular Dynamics (MD) is a computational method used to model the physical movements of atoms and molecules. In the context of PyMembrane, MD integrators simulate the dynamics of coarse-grained systems. These integrators are especially valuable when considering thermal fluctuations or the dynamics of interacting particles. The Evolver class incorporates the capability to include Molecular Dynamics integrators to handle the evolution of the system under various physical interactions.
Parameters and MD Integrators#
Molecular Dynamics integrators in PyMembrane are added to the system using the add_integrator method of the Evolver class. Like other integrators and force potentials, parameters for MD integrators are passed in a dictionary format.
The typical format to add an MD integrator is:
evolver.add_integrator("<MD_IntegratorName>", {"<Parameter1>": "<Value1>",
"<Parameter2>": "<Value2>",
...})
A quick breakdown of the components:
<MD_IntegratorName>: The specific name of the Molecular Dynamics integrator.
<Parameter1>, <Parameter2>, …: Parameters that guide the behavior of the integrator.
<Value1>, <Value2>, …: The corresponding values for the parameters, typically passed as strings.
Example#
Consider the following example:
evolver.add_integrator("Mesh>brownian", {"T": "0.2"})
In this example: - The integrator, “Mesh>brownian”, represents a Brownian dynamics simulation, which models the random motion of particles suspended in a fluid resulting from their collision with the quick atoms or molecules in the gas or liquid. - The parameter “T” denotes the temperature of the system and is set to a value of “0.2” (in appropriate units).