htmd.protocols.production_v5 module

class htmd.protocols.production_v5.Production

Bases: htmd.protocols.oldprotocolinterface.ProtocolInterface

Warning

Deprecated since version 1.13.6.

Production protocol v5

Production protocol for globular and membrane proteins. You can optionally define a flatbottom potential box and atom constraints for the production run.

runtimefloat, default=0

Running time of the simulation.

timeunitsstr, default=’steps’

Units for runtime. Can be ‘steps’, ‘ns’ etc.

temperaturefloat, default=300

Temperature of the thermostat in Kelvin

fb_kfloat, default=0

Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5

fb_referencestr, default=’none’

Reference selection to use as dynamic center of the flatbottom box.

fb_selectionstr, default=’none’

Selection of atoms to apply the flatbottom potential

fb_boxlist, default=[0, 0, 0, 0, 0, 0]

Position of the flatbottom box in term of the reference center given as [xmin, xmax, ymin, ymax, zmin, zmax]

useconstantratiobool, default=False

For membrane protein simulations set it to true so that the barostat does not modify the xy aspect ratio.

useconstraintsbool, default=False

Apply constraints to the production simulation, defined by the constraints parameter

constraintsdict, default={}

A dictionary of atomselections and values of the constraint to be applied (in kcal/mol/A^2). Atomselects must be mutually exclusive.

adaptivebool, default=False

Set to True if making production runs for adaptive sampling.

addConstraint(atomselect, factor=1)

Convenience function for adding a new constraint to existing constraints.

Parameters

  • atomselect (str) – Atom selection of atoms we want to constrain

  • factor (float) – The scaling factor of the constraints applied to the atoms

Example

>>> eq.addConstraint('chain X', 0.3)
write(inputdir, outputdir)

Writes the production protocol and files into a folder.

Parameters

  • inputdir (str) – Path to a directory containing the files produced by a equilibration process.

  • outputdir (str) – Directory where to write the production setup files.