htmd.protocols.pmemdequilibration module

class htmd.protocols.pmemdequilibration.Equilibration(**kwargs)

Bases: htmd.protocols.oldprotocolinterface.ProtocolInterface

Warning

Deprecated since version 1.13.6.

Equilibration protocol

Equilibration protocol for globular and membrane proteins It includes a flatbottom potential box to retrain a ligand for example within this box.

numstepsint, default=0

Number of steps to run the simulations in units of 4fs

temperaturefloat, default=300

Temperature of the thermostat in Kelvin

kfloat, default=0

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

referencestr, default=’none’

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

selectionstr, default=’none’

Selection of atoms to apply the flatbottom potential

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.

constraintsdict, default={‘protein and noh and not name CA’: 0.1, ‘protein and name CA’: 1}

A dictionary containing as keys the atomselections of the constraints and as values the constraint scaling factor. 0 factor means no constraint, 1 full constraints and in between values are used for scaling. The order with which the constraints are applied is random, so make atomselects mutually exclusive to be sure you get the correct constraints.

>>> from htmd.protocols.equilibration_v1 import Equilibration
>>> md = Equilibration()
>>> md.numsteps = 10000000
>>> md.temperature = 300
>>> md.useconstantratio = True  # only for membrane sims
>>> # this is only needed for setting the flatbottom potential, otherwise remove it
>>> md.reference = 'protein and resid 293'
>>> md.selection = 'segname L and noh'
>>> md.box = [-25, 25, -25, 25, 43, 45]
>>> md.k = 5
>>> md.write('./build','./equil')
write(inputdir, outputdir)

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.

Examples

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