The umbrella integration algorithm.
Project description
Umbrella Integration[1] algorithm of calculating PMF using Python.
Dependence
Python3
Numpy
pandas for parsing metafile
Scipy for trapz integration
Usage:
See help:
python3 ubint.py -hInput
Metafile
The <your-metafile> should be in fellowing form:
/path/to/your/window/file window_center spring_constant [temperature]There is a variable of T in ubint.py, if the temperature left blank in the metafile, the default temperature would be variable T in the ubint.py, or you can set specific temperature for some window.
Data file for each window
The data file of each window need to be a 2-column file with time reaction_coordinate, the coordinate should be 1-dimensional.
Output
The output file is free_py.txt with 2-column reaction_coordinate free_energy
Warning
Unit
I use kJ/mol in this program.
Spring constant K
In your simulation, the biased spring potential shoud be in form of 0.5 * K * (r - r0) ** 2, here K is the parameter set in your <your-metafile>, for some simulation program, there is no 0.5 in the biased spring potential.
Screen shots
Raw data was generated by Gaussian distribution for each window with MEAN=window_center and STD=0.8, the centers are in range of 0.0 ~ 19.5 by step of 0.5, here is the result compare with WHAM[2]:
Raw Data
Compare with WHAM
The zero point in WHAM is the minimum value and the zero point in UI is 0.
TO DO
The UI algorithm with higher oder terms[3] of A(xi) is ubint_ho_devel.py, the result is not ideal using previous data, still in development.
Problems occurred at standard normal distributions, maybe the quadruplicate term which even possesses a small value could cause a huge deviation. I should try some systems with non-quadratic potentials.
The function ``exp(-beta(a1*xi+a2*xi^2+a3*xi^3+a4*xi^4))`` and its integration (Normalization factor) give very large value (even inf), this is unable to solve yet.
Results
Ref
Kästner, Johannes, and Walter Thiel. “Bridging the Gap between Thermodynamic Integration and Umbrella Sampling Provides a Novel Analysis Method: ‘Umbrella Integration.’” The Journal of Chemical Physics 123, no. 14 (October 8, 2005): 144104. doi:10.1063/1.2052648.
Kästner, Johannes. “Umbrella Integration with Higher-Order Correction Terms.” The Journal of Chemical Physics 136, no. 23 (June 21, 2012): 234102. doi:10.1063/1.4729373.
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