htmd.protocols.pmemdproduction module

class htmd.protocols.pmemdproduction.Production

Bases: htmd.protocols.oldprotocolinterface.ProtocolInterface

Warning

Deprecated since version 1.13.6.

Production protocol for globular and membrane proteins

>>> 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')