schrodinger.application.matsci.desmondutils.MDMSJStringer

Class MDMSJStringer

object --+ | MSJStringer --+ | MDMSJStringer

An MSJStringer class for Molecular Dynamics stages

Instance Methods

__init__(self, time=None, temp=None, pressure=None, ensemble='NPT', method=None, timestep=None, last=False, **kwargs)
Create a MDMSJStringer object

str

getTitle(self)
Return a title for the stage describing the main parameters.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Create a MDMSJStringer object

Any keyword that does not have a value supplied will use the default Desmond value for MD simulations.

Parameters:

time (float) - Time in picoseconds
temp (float) - Temperature in Kelvin
pressure (float) - The pressure in bar
ensemble (str) - Valid Desmond ensemble such as NPT, NVT
method (str) - Valid Desmond ensemble method such as NH, Berendson, Langevin
timestep (str or list) - The timestep in picoseconds, either as a list of three floats or a string. If a string, it is used directly so must be in the proper [ x y z ] format used in .msj and .cfg files.
last (bool) - Whether the msj lines typically associated with the last stage (dir, compress) should be included
All other keyword arguments are turned into lines in the .msj file. See parent class for additional information.

Overrides: object.__init__

Return a title for the stage describing the main parameters.

Class MDMSJStringer