htmd.protocols.production_v1 module¶

class htmd.protocols.production_v1.Production¶

Warning

Deprecated since version 1.13.6.: Production protocol for globular and membrane proteins

It also includes a possible flatbottom potential 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]

write(inputdir, outputdir)¶

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.