htmd.adaptive.adaptive.
AdaptiveBase
¶Bases: abc.ABC
, protocolinterface.protocolinterface.ProtocolInterface
run
()¶Runs the adaptive
Use this command to start the adaptive.
Example
>>> adapt = Adaptive()
>>> adapt.run()
htmd.adaptive.adaptive.
epochSimIndexes
(simlist)¶Finds the simulation indexes for each epoch.
Creates a dictionary with the epoch number as key and values the simlist indexes of the simulations corresponding to the given epoch.
htmd.adaptive.adaptive.
getEpochFromName
(name)¶Given a adaptive simulation name, tells you which epoch it belongs to.
htmd.adaptive.adaptive.
reconstructAdaptiveTraj
(simlist, trajID)¶Reconstructs a long trajectory out of short adaptive runs.
mol (Molecule
object) – A Molecule object containing the reconstructed trajectory
chain (np.ndarray) – The simulation IDs of all simulations involved
pathlist (np.ndarray of str) – The names of all simulations involved.
Examples
>>> mol, chain, pathlist = reconstructAdaptiveTraj(data.simlist, 52)