pyPRISM.calculate.pmf module

pyPRISM.calculate.pmf.pmf(PRISM)

Calculate the potentials of mean force

Parameters:PRISM (pyPRISM.core.PRISM) – A solved PRISM object. Returns:pmf – The full MatrixArray of potentials of mean force Return type:pyPRISM.core.MatrixArray

Mathematical Definition

\[w_{\alpha,\beta}(r) = -k_{B} T \ln(h_{\alpha,\beta}(r)+1.0)\]

Variable Definitions

• \(w_{\alpha,\beta}(r)\)

  Potential of mean force between site types \(\alpha\) and \(\beta\) at a distance \(r\)

• \(g_{\alpha,\beta}(r)\)

  Pair correlation function between site types \(\alpha\) and \(\beta\) at a distance \(r\)

• \(h_{\alpha,\beta}(r)\)

  Total correlation function between site types \(\alpha\) and \(\beta\) at a distance \(r\)

Description

A potential of mean force (PMF) between site types \(\alpha\) and \(\beta\), \(w_{\alpha,\beta}\) represents the the ensemble averaged free energy change needed to bring these two sites from infinite separation to a distance \(r\). It can also be thought of as a potential that would be needed to reproduce the underlying \(g_{\alpha,\beta}(r)\).

Warning

Passing an unsolved PRISM object to this function will still produce output based on the default values of the attributes of the PRISM object.

Example

import pyPRISM

sys = pyPRISM.System(['A','B'])

# ** populate system variables **

PRISM = sys.createPRISM()

PRISM.solve()

pmf = pyPRISM.calculate.pmf(PRISM)

pmf_BB = pmf['B','B']