Alchemical Analysis: An open tool implementing some recommended practices for analyzing alchemical free energy calculations
We are in the process of migrating all functionality from here to instead use alchemlyb, which focuses on being a general Python library for performing analysis of alchemical calculations rather than a stand-alone command-line tool for analyzing these calculations.
We recommend you move to using, and contribute to the development of, alchemlyb instead.
It already has the following advantages, among others:
- Python 3 compatible
- Works as a library rather than a stand-alone tool, allowing easier connection with trajectory analysis
- Has automated testing/continuous integration testing
- Easily extensible
However, some of the plotting functionality and analysis features available in alchemical analysis are not yet available in alchemlyb.
If there is functionality which is particularly important to you which is missing there, please raise an issue on the alchemlyb issue tracker.
In the meantime, Alchemical Analysis is still available but deprecated and we discourage its use. Please use alchemlyb instead. We may occasionally perform minor/critical maintenance here, but intend to cease maintaining this package over time.
Analyze alchemical free energy calculations conducted in GROMACS, AMBER or SIRE using recommended best practices from Klimovich et al., JCAMD 29:397-411 (2015).
This tool handles analysis via a slate of free energy methods, including BAR, MBAR, TI, and the Zwanzig relationship (exponential averaging) among others, and provides a good deal of analysis of computed free energies and convergence in order to help you assess the quality of your results.
If you have problems with this tool, please use the github issue tracker.
Alchemical Analysis is research software. If you make use of it in work which you publish, please cite it. The BibTex reference is
@article{Klimovich:2015er,
author = {Klimovich, Pavel V and Shirts, Michael R and Mobley, David L},
title = {Guidelines for the analysis of free energy calculations},
journal = {J Comput Aided Mol Des},
year = {2015},
volume = {29},
number = {5},
pages = {397--411},
doi = {10.1007/s10822-015-9840-9}
}
Alchemical Analysis requires the pymbar module (we recommend
installation via conda, but other options are also available). Version
3.0.0.dev0 or above is required. The latest version of pymbar can be found
here.
Python 2 is required.
git clone https://github.com/MobleyLab/alchemical-analysis.git
cd alchemical-analysis
sudo python setup.py install
Script: alchemical_analysis
This implements recommended practices for analyzing alchemical free energy calculations, as described in Klimovich et al., JCAMD 29:397-411 (2015). This was motivated in part by earlier work illustrating how to apply MBAR to alchemical free energy calculations (and a comparison with other methods) in Paliwal and Shirts, J. Chem. Theory Comp, v. 7, 4115-4134 (2011).
See description in samples/gromacs/README.md, samples/sire/README.md, and samples/amber/README.md.
Help for alchemical_analysis.py (obtained with alchemical_analysis -h) is:
-h, --help show this help message and exit
-a SOFTWARE, --software=SOFTWARE
Package's name the data files come from: Gromacs,
Sire, Desmond, or AMBER. Default: Gromacs.
-b FRACTION, --fraction=FRACTION
The fraction of the energy file will be used to
calculate the statistics. Default: 1.0
-c, --cfm The Curve-Fitting-Method-based consistency inspector.
Default: False.
-d DATAFILE_DIRECTORY, --dir=DATAFILE_DIRECTORY
Directory in which data files are stored. Default:
Current directory.
-e, --backward Extract the energy data from the backward direction.
Default: False
-f BFORWREV, --forwrev=BFORWREV
Plot the free energy change as a function of time in
both directions, with the specified number of points
in the time plot. The number of time points (an
integer) must be provided. Default: 0
-g, --breakdown Plot the free energy differences evaluated for each
pair of adjacent states for all methods, including the
dH/dlambda curve for TI. Default: False.
-i UNCORR_THRESHOLD, --threshold=UNCORR_THRESHOLD
Proceed with correlated samples if the number of
uncorrelated samples is found to be less than this
number. If 0 is given, the time series analysis will
not be performed at all. Default: 50.
-j RESULTFILENAME, --resultfilename=RESULTFILENAME
custom defined result filename prefix. Default:
results
-k BSKIPLAMBDAINDEX, --koff=BSKIPLAMBDAINDEX
Give a string of lambda indices separated by '-' and
they will be removed from the analysis. (Another
approach is to have only the files of interest present
in the directory). Default: None.
-m METHODS, --methods=METHODS
A list of the methods to esitimate the free energy
with. Default: [TI, TI-CUBIC, DEXP, IEXP, BAR, MBAR].
To add/remove methods to the above list provide a
string formed of the method strings preceded with +/-.
For example, '-ti_cubic+gdel' will turn methods into
[TI, DEXP, IEXP, BAR, MBAR, GDEL]. 'ti_cubic+gdel', on
the other hand, will call [TI-CUBIC, GDEL]. 'all'
calls the full list of supported methods [TI, TI-
CUBIC, DEXP, IEXP, GINS, GDEL, BAR, UBAR, RBAR, MBAR].
-n UNCORR, --uncorr=UNCORR
The observable to be used for the autocorrelation
analysis; either 'dhdl_all' (obtained as a sum over
all energy components) or 'dhdl' (obtained as a sum
over those energy components that are changing;
default) or 'dE'. In the latter case the energy
differences dE_{i,i+1} (dE_{i,i-1} for the last
lambda) are used.
-o OUTPUT_DIRECTORY, --out=OUTPUT_DIRECTORY
Directory in which the output files produced by this
script will be stored. Default: Same as
datafile_directory.
-p PREFIX, --prefix=PREFIX
Prefix for datafile sets, i.e.'dhdl' (default).
-q SUFFIX, --suffix=SUFFIX
Suffix for datafile sets, i.e. 'xvg' (default).
-r DECIMAL, --decimal=DECIMAL
The number of decimal places the free energies are to
be reported with. No worries, this is for the text
output only; the full-precision data will be stored in
'results.pickle'. Default: 3.
-s EQUILTIME, --skiptime=EQUILTIME
Discard data prior to this specified time as
'equilibration' data. Units picoseconds. Default: 0
ps.
-t TEMPERATURE, --temperature=TEMPERATURE
Temperature in K. Default: 298 K.
-u UNITS, --units=UNITS
Units to report energies: 'kJ', 'kcal', and 'kBT'.
Default: 'kJ'
-v, --verbose Verbose option. Default: False.
-w, --overlap Print out and plot the overlap matrix. Default: False.
-x, --ignoreWL Do not check whether the WL weights are equilibrated.
No log file needed as an accompanying input.
-y RELATIVE_TOLERANCE, --tolerance=RELATIVE_TOLERANCE
Convergence criterion for the energy estimates with
BAR and MBAR. Default: 1e-10.
-z INIT_WITH, --initialize=INIT_WITH
The initial MBAR free energy guess; either 'BAR' or
'zeros'. Default: 'BAR'.
MIT.