htmd.protocols.pmemdproduction.
Production
(**kwargs)¶Bases: htmd.protocols.oldprotocolinterface.ProtocolInterface
Warning
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
Examples
>>> md = Equilibration()
>>> md.write('./build','./equil')