htmd.protocols.equilibration_v3 module#

class htmd.protocols.equilibration_v3.Equilibration#

Bases: ProtocolInterface

Equilibration protocol v3

Equilibration protocol for globular and membrane proteins Supporst extra restraints like a flatbottom potential box to retain a ligand for example within this box.

Parameters
  • runtime (float, default=0) – Running time of the simulation.

  • timeunits (str, default='steps') – Units for time arguments. Can be ‘steps’, ‘ns’ etc.

  • temperature (float, default=300) – Temperature of the thermostat in Kelvin

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

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

  • restraintsteps (int, default=None) – Number of initial steps to apply restraints in units of 4fs. Defaults to half the simulation time.

Example

>>> from htmd.protocols.equilibration_v3 import Equilibration
>>> from htmd.mdengine.acemd.acemd import GroupRestraint
>>> md = Equilibration()
>>> md.runtime = 4
>>> md.timeunits = 'ns'
>>> md.temperature = 300
>>> md.useconstantratio = True  # only for membrane sims
Use a 10A flat bottom potential to prevent the ligand from diffusing from original position during equilibration
>>> width = np.array([10, 10, 10])
>>> flatbot = GroupRestraint('segname L and noh', width, [(5, '0ns')])
Add also the default restraints for protein
>>> mol = Molecule("./build/structure.pdb")
>>> md.restraints = [flatbot,] + md.defaultEquilRestraints('2ns', mol)
>>> md.write('./build','./equil')
defaultEquilRestraints(decay, mol=None)#

Get the default equilibration restraints

Parameters

decay (str) – The restrains will get scaled to 0 over this much time.

Returns

restraints – A list of default protein restraints

Return type

list

Examples

>>> md = Equilibration()
>>> res = md.defaultEquilRestraints('20ns')
write(inputdir, outputdir, cisbondcheck=True)#

Write the equilibration protocol

Writes the equilibration protocol and files into a folder for execution using files inside the inputdir directory

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

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

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

Examples

>>> md = Equilibration()
>>> md.write('./build','./equil')