openpathsampling.collectivevariables.PLUMEDInterface

class openpathsampling.collectivevariables.PLUMEDInterface(topology, pathtoplumed='', timestep=1.0, kbt=1.0, molinfo='', logfile='plumed.log')[source]

Interfaces the Cython PLUMED wrapper [PLU2b] located at /path/to/plumed2/python and allows to set and get non-PLUMEDCV commands (i.e., non-outputting). This includes groups of atoms, centers of mass, include files, etc. Requires PLUMED development version (see https://github.com/plumed/plumed2) and sourcing /path/to/plumed2/sourceme.sh.

References

[PLU2b]

G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED2: New feathers for an old bird, Comp. Phys. Comm. 185, 604 (2014); https://doi.org/10.1016/j.cpc.2013.09.018

Examples

>>> # To group the atoms [7,9,15,17] corresponding to the dihedral psi
>>> # in Ala dipeptide:
>>> from openpathsampling import PLUMEDCV, PLUMEDInterface
>>> plmd = PLUMEDInterface(top)
>>> # top is an `openpathsampling.engines.topology.MDTrajTopology`
>>> plmd.set("group","GROUP ATOMS=7,9,15,17")
>>> psi_plumed = PLUMEDCV("psi",plmd,"TORSION ATOMS=group")
>>> print psi_plumed(traj)  # returns psi values for the trajectory
>>> pld.get()  # returns (('group', 'GROUP ATOMS=7,9,15,17'))

__init__(topology, pathtoplumed='', timestep=1.0, kbt=1.0, molinfo='', logfile='plumed.log')[source]

Parameters:

topology (openpathsampling.engines.topology.MDTrajTopology)
pathtoplumed (string) – path to the PLUMED installation
timestep (double) – Time step size of the simulation in PLUMED default units (ps).
kbt (double) – $$k_BT$$ in PLUMED default units (kJ/mol).
molinfo (string) – A PDB file containing information about the molecule. (see https://plumed.github.io/doc-v2.4/user-doc/html/_m_o_l_i_n_f_o.html).
logfile (string) – Name of the PLUMED log file.

Methods

`__init__`(topology[, pathtoplumed, timestep, ...])
`args`()	Return a list of args of the __init__ function of a class
`base`()	Return the most parent class actually derived from StorableObject
`cmd`(args, *kwargs)
`count_weaks`()	Return number of objects subclassed from StorableObject still in memory
`descendants`()	Return a list of all subclassed objects
`fix_name`()	Set the objects name to be immutable.
`from_dict`(dct)	Reconstruct an object from a dictionary representaiton
`get`()	Get commands set in the PLUMEDInterface.
`get_uuid`()
`idx`(store)	Return the index which is used for the object in the given store.
`named`(name)	Name an unnamed object.
`objects`()	Returns a dictionary of all storable objects
`reverse_uuid`()
`ruuid`(uid)
`set`(name, definition)	Set a non-outputting command in the PLUMEDInterface.
`set_observer`(active)	(De-)Activate observing creation of storable objects
`to_dict`()	Convert object into a dictionary representation

Attributes

`ACTIVE_LONG`
`CREATION_COUNT`
`INSTANCE_UUID`
`base_cls`	Return the base class
`base_cls_name`	Return the name of the base class
`cls`	Return the class name as a string
`default_name`	Return the default name.
`is_named`	True if this object has a custom name.
`name`	Return the current name of the object.
`observe_objects`