4.7.1. Polymer analysis — MDAnalysis.analysis.polymer
- Author:
Richard J. Gowers
- Year:
2015, 2018
- Copyright:
Lesser GNU Public License v2.1+
This module contains various commonly used tools in analysing polymers.
- class MDAnalysis.analysis.polymer.PersistenceLength(atomgroups, **kwargs)[source]
Calculate the persistence length for polymer chains
The persistence length is the length at which two points on the polymer chain become decorrelated. This is determined by first measuring the autocorrelation (\(C(n)\)) of two bond vectors (\(\mathbf{a}_i, \mathbf{a}_{i + n}\)) separated by \(n\) bonds
\[C(n) = \langle \cos\theta_{i, i+n} \rangle = \langle \mathbf{a_i} \cdot \mathbf{a_{i+n}} \rangle\]An exponential decay is then fitted to this, which yields the persistence length
\[C(n) \approx \exp\left( - \frac{n \bar{l_B}}{l_P} \right)\]where \(\bar{l_B}\) is the average bond length, and \(l_P\) is the persistence length which is fitted
- Parameters:
atomgroups (iterable) – List of AtomGroups. Each should represent a single polymer chain, ordered in the correct order.
verbose (bool, optional) – Show detailed progress of the calculation if set to
True.
- results.bond_autocorrelation
the measured bond autocorrelation
- Type:
- lb
Alias to the
results.lb.Deprecated since version 2.0.0: Will be removed in MDAnalysis 3.0.0. Please use
results.lbinstead.- Type:
- results.x
length of the decorrelation predicted by lp
Added in version 2.0.0.
- Type:
- lp
Alias to the
results.lp.Deprecated since version 2.0.0: Will be removed in MDAnalysis 3.0.0. Please use
results.lpinstead.- Type:
- results.fit
the modelled backbone decorrelation predicted by lp
Added in version 2.0.0.
- Type:
- fit
Alias to the
results.fit.Deprecated since version 2.0.0: Will be removed in MDAnalysis 3.0.0. Please use
results.fitinstead.- Type:
See also
sort_backbone()for producing the sorted AtomGroup required for input.
Example
from MDAnalysis.tests.datafiles import TRZ_psf, TRZ import MDAnalysis as mda from MDAnalysis.analysis import polymer u = mda.Universe(TRZ_psf, TRZ) # this system is a pure polymer melt of polyamide, # so we can select the chains by using the .fragments attribute chains = u.atoms.fragments # select only the backbone atoms for each chain backbones = [chain.select_atoms('not name O* H*') for chain in chains] # sort the chains, removing any non-backbone atoms sorted_backbones = [polymer.sort_backbone(bb) for bb in backbones] persistence_length = polymer.PersistenceLength(sorted_backbones) # Run the analysis, this will average over all polymer chains # and all timesteps in trajectory persistence_length = persistence_length.run() print(f'The persistence length is: {persistence_length.results.lp}') # always check the visualisation of this: persistence_length.plot()
Added in version 0.13.0.
Changed in version 0.20.0: The run method now automatically performs the exponential fit
Changed in version 1.0.0: Deprecated
PersistenceLength.perform_fit()has now been removed.
- MDAnalysis.analysis.polymer.fit_exponential_decay(x, y)[source]
Fit a function to an exponential decay
\[y = \exp\left(- \frac{x}{a}\right)\]- Parameters:
x (array_like) – The two arrays of data
y (array_like) – The two arrays of data
- Returns:
a – The coefficient a for this decay
- Return type:
Notes
This function assumes that data starts at 1.0 and decays to 0.0
- MDAnalysis.analysis.polymer.sort_backbone(backbone)[source]
Rearrange a linear AtomGroup into backbone order
Requires that the backbone has bond information, and that only backbone atoms are provided (ie no side chains or hydrogens).
- Parameters:
backbone (AtomGroup) – the backbone atoms, not necessarily in order
- Returns:
sorted_backbone – backbone in order, so sorted_backbone[i] is bonded to sorted_backbone[i - 1] and sorted_backbone[i + 1]
- Return type:
Added in version 0.20.0.