Tutorial

In this tutorial, we will demonstrate how to use alchemlyb with test data from alchemtest. This guide provides a general introduction to the tool with minimal explanations. For more detailed information, please refer to the relevant sections of the documentation.

Parsing the Free Energy Data

alchemlyb requires free energy data obtained from alchemical simulations. In this example, we use free energy data from Gromacs. Instructions for reading data from other MD engines are available in the documentation on parsing files. We load the free energy data into a pandas.DataFrame:

>>> from alchemtest.gmx import load_benzene
>>> from alchemlyb.parsing.gmx import extract_u_nk

>>> bz = load_benzene().data
>>> u_nk_list = [extract_u_nk(xvg, T=300) for xvg in bz['Coulomb']]
>>> u_nk_list[0]
                         0.0      0.25       0.5       0.75        1.0
time    fep-lambda
0.0     0.0         0.309323  3.656838  7.004353  10.351867  13.699382
10.0    0.0         0.308844  2.616688  4.924532   7.232375   9.540219
20.0    0.0         0.300940  1.626739  2.952538   4.278337   5.604135
30.0    0.0         0.309712  1.579647  2.849583   4.119518   5.389453
40.0    0.0         0.299979  2.255386  4.210794   6.166202   8.121609
...                      ...       ...       ...        ...        ...
39960.0 0.0         0.309339  2.999887  5.690435   8.380983  11.071532
39970.0 0.0         0.304674  2.313761  4.322848   6.331935   8.341022
39980.0 0.0         0.305687  2.047583  3.789479   5.531375   7.273271
39990.0 0.0         0.303546  3.174116  6.044686   8.915256  11.785826
40000.0 0.0         0.314376  3.021203  5.728030   8.434858  11.141684

[4001 rows x 5 columns]

Decorrelating the Data

The MBAR estimator requires decorrelated data. Various options for decorrelating the data are available in the relevant documentation on subsampling data. Here, we decorrelate the data using the following code.

>>> from alchemlyb.preprocessing.subsampling import decorrelate_u_nk

>>> decorrelated_u_nk_list = [decorrelate_u_nk(u_nk) for u_nk in u_nk_list]
>>> decorrelated_u_nk_list[0]
                         0.0      0.25       0.5       0.75        1.0
time    fep-lambda
0.0     0.0         0.309323  3.656838  7.004353  10.351867  13.699382
20.0    0.0         0.300940  1.626739  2.952538   4.278337   5.604135
40.0    0.0         0.299979  2.255386  4.210794   6.166202   8.121609
60.0    0.0         0.308315  2.284146  4.259977   6.235809   8.211640
80.0    0.0         0.301432  1.397817  2.494203   3.590589   4.686975
...                      ...       ...       ...        ...        ...
39920.0 0.0         0.305202  2.420299  4.535396   6.650492   8.765589
39940.0 0.0         0.307156 -0.552737 -1.412630  -2.272523  -3.132416
39960.0 0.0         0.309339  2.999887  5.690435   8.380983  11.071532
39980.0 0.0         0.305687  2.047583  3.789479   5.531375   7.273271
40000.0 0.0         0.314376  3.021203  5.728030   8.434858  11.141684

[2001 rows x 5 columns]

Estimating Free Energy

We estimate the free energy using the MBAR method. More estimators are available in the section on free energy estimators.

>>> from alchemlyb.estimators import MBAR
>>> import pandas as pd

>>> mbar = MBAR()
>>> mbar.fit(alchemlyb.concat(decorrelated_u_nk_list))
>>> mbar.delta_f_
          0.00      0.25      0.50      0.75      1.00
0.00  0.000000  1.613595  2.553407  2.983336  3.039517
0.25 -1.613595  0.000000  0.939812  1.369741  1.425922
0.50 -2.553407 -0.939812  0.000000  0.429929  0.486110
0.75 -2.983336 -1.369741 -0.429929  0.000000  0.056181
1.00 -3.039517 -1.425922 -0.486110 -0.056181  0.000000

Free energy difference between \(\lambda = 0\) and \(\lambda = 1\) is

>>> mbar.delta_f_.loc[0.00, 1.00]
3.039517

Plotting the Diagnostics

We can plot the diagnostics of the estimator to assess the overlap metrics. More information on diagnostics is available in the relevant section on visualisation:

>>> from alchemlyb.visualisation import plot_mbar_overlap_matrix
>>> ax = plot_mbar_overlap_matrix(mbar.overlap_matrix)
>>> ax.figure.savefig('O_MBAR.pdf', bbox_inches='tight', pad_inches=0.0)

This will generate a plot that looks like the one below:

_images/O_MBAR.png

Automated workflow

The above manual workflow can be automated using the ABFE workflow class, which demonstrates a best practice implementation for using alchemlyb in a end-to-end fashion.

See also

See the ABFE workflow section of the documentation for more details on how to use ABFE.

Absolute binding free energy (ABFE) calculations can be analyzed with two lines of code in a fully automated manner. All parameters are set when invoking ABFE and reasonable defaults are chosen for any parameters not set explicitly. The two steps are to

  1. initialize an instance of the ABFE class

  2. invoke the run() method to execute the complete workflow.

As an example, we again use data from a GROMACS ABFE simulation that is available in alchemtest. In this case, executing the workflow would look similar to the following code

>>> from alchemtest.gmx import load_ABFE
>>> from alchemlyb.workflows import ABFE
>>> # Obtain the path of the data
>>> import os
>>> dir = os.path.dirname(load_ABFE()['data']['complex'][0])
>>> print(dir)
'alchemtest/gmx/ABFE/complex'
>>> workflow = ABFE(units='kcal/mol', software='GROMACS', dir=dir,
>>>                 prefix='dhdl', suffix='xvg', T=298, outdirectory='./')
>>> workflow.run(skiptime=10, uncorr='dhdl', threshold=50,
>>>              estimators=('MBAR', 'BAR', 'TI'), overlap='O_MBAR.pdf',
>>>              breakdown=True, forwrev=10)

The workflow uses parsing to parse the data from the energy files, remove the initial un-equilibrated frames and decorrelate the data with subsampling. The decorrelated datasets dHdl and u_nk are then passed to estimators for free energy estimation. The workflow will also perform a set of analysis that allows the user to examine the quality of the estimation.