htmd.protocols.production_v6 module

class htmd.protocols.production_v6.Production(_version=2)

Bases: protocolinterface.protocolinterface.ProtocolInterface

Production protocol v6

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

An Acemd class object is stored in the Production object which can be used to modify futher options. For documentation on further options see Acemd

Parameters:
  • runtime (float, default=0) – Running time of the simulation.
  • timeunits (str, default='steps') – Units for runtime. Can be ‘steps’, ‘ns’ etc.
  • temperature (float, default=300) – Temperature of the thermostat in Kelvin
  • fb_k (float, default=0) – Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5
  • fb_reference (str, default='none') – Reference selection to use as dynamic center of the flatbottom box.
  • fb_selection (str, default='none') – Selection of atoms to apply the flatbottom potential
  • fb_box (list, 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]
  • useconstantratio (bool, default=False) – For membrane protein simulations set it to true so that the barostat does not modify the xy aspect ratio.
  • useconstraints (bool, default=False) – Apply constraints to the production simulation, defined by the constraints parameter
  • constraints (dict, default={}) – A dictionary of atomselections and values of the constraint to be applied (in kcal/mol/A^2). Atomselects must be mutually exclusive.
  • adaptive (bool, 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.