htmd.apps.pmemd module

class htmd.apps.pmemd.Pmemd(**kwargs)

Bases: htmd.protocols.oldprotocolinterface.ProtocolInterface

Warning

Deprecated since version 1.13.6.

load(path='.')

Loads all files required to run a simulation and apply eventually configured protocols to it

Parameters

path (str) – Working directory relative to which the configuration file is read

save(path, overwrite=False)

Create a directory with all necessary input to run with AMBER.

Parameters
  • path (str) – New execution directory to create

  • overwrite (bool) – Overwrite output directory if it exists.

setup(cwd='./', outdir='./run', overwrite=False)

Convenience method performing load and save.

Parameters
  • cwd (str) – The directory to load from.

  • outdir (str) – The directory to save to.

  • overwrite (bool) – Overwrite output directory if it exists.

show(quiet=False)

Returns the AMBER configuration file string

Parameters

quiet (bool) – If true it prints the string to stdout

Returns

conf – The string of the configuration file

Return type

str

writeConf(fname='input')

Write an acemd configuration file

Parameters

fname (output file name) –