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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 -h

Input

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
Raw Raw
Raw IL
  • Compare with WHAM
CMP CMP

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

CMP\_HO CMP\_HO

Ref

  1. 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.
  2. http://membrane.urmc.rochester.edu/content/wham
  3. 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.

Project details


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This version

0.41

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