htmd.protocols.production_v2 module

class htmd.protocols.production_v2.Production(**kwargs)

Bases: htmd.protocols.oldprotocolinterface.ProtocolInterface


Deprecated since version 1.13.6.

Production protocol for globular and membrane proteins

It also includes a possible flatbottom potential box

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]

write(inputdir, outputdir)

Writes the production protocol and files into a folder.

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

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