htmd.protocols.production_v6 module#

class htmd.protocols.production_v6.Production#

Bases: 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

  • useconstantratio (bool, default=False) – For membrane protein simulations set it to true so that the barostat does not modify the xy aspect ratio.

  • restraints (list, default=None) – A list of restraint objects. See AtomRestraint and GroupRestraint)

  • adaptive (bool, default=False) – Set to True if making production runs for adaptive sampling.

Example

>>> from htmd.protocols.production_v6 import Production
>>> from htmd.mdengine.acemd.acemd import GroupRestraint
>>> md = Production()
>>> md.runtime = 4
>>> md.timeunits = 'ns'
>>> md.temperature = 300
>>> md.useconstantratio = True  # only for membrane sims
Use a 10x10x30A flat bottom potential centered on protein residue 142 to prevent the ligand from crossing periodic boxes
ending up on the other side of the membrane.
>>> width = [10, 10, 30]
>>> flatbot = GroupRestraint('segname L and noh', width, [(5, '0ns')], fbcentersel="protein and resid 142")
>>> md.restraints = flatbot
>>> md.write('./build','./equil')
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, cisbondcheck=True)#

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.

  • cisbondcheck (bool) – Set to False to disable the cis peptidic bond checks