BioSimSpace.Protocol¶
The Protocol package contains functionality for defining generic molecular
dynamics protocols. The protocols contain configurable options that are
common across different molecular dynamics packages. In combination with a
molecular System
, protocols can
be used to create a molecular dynamics Process
.
Functions¶
Return a list of the supported Molecular Dynamics protocols. |
|
|
Create a default simulation protocol. |
Classes¶
|
A class for storing custom protocols. |
|
A class for storing equilibration protocols. |
|
A class for storing free energy protocols. |
|
A class for storing metadynamics protocols. |
|
A class for storing minimisation protocols. |
|
A class for storing production protocols. |
|
A class for storing steered molecular dynamics protocols. |
Examples
Print the list of supported protocols.
import BioSimSpace as BSS
print(BSS.Protocol.protocols())
Create a default minimisation protocol and print the number of steps.
import BioSimSpace as BSS
protocol = BSS.Protocol.Minimisation()
print(protocol.getSteps())
The same as above, but instead passing “Minimisation” as an argument to the
createProtocol
function. This
function should be used in any interoperable workflow
Node
where the protocol is specified
as an input requirement by the user.
import BioSimSpace as BSS
protocol = BSS.Protocol.createProtocol("minimisation")
print(protocol.getSteps())
Create an equilibration protocol that heats the system from 0 to 300 Kelvin while restraining the positions of any backbone atoms.
import BioSimSpace as BSS
protocol = BSS.Protocol.Equilibration(temperature_start=0*BSS.Units.Temperature.kelvin,
temperature_end=300*BSS.Units.Temperature.kelvin,
restraint="backbone")