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README

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Daniel Bauer
2020-10-25 20:49:52 +01:00
parent b9d08ae24b
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README.md
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@@ -14,6 +14,7 @@ Features
- Fast, especially for small systems - Fast, especially for small systems
- Multithreaded - Multithreaded
- Multidimensional - Multidimensional
- Autocorrelation to remove correlated samples
- Error analysis - Error analysis
- Unit tested - Unit tested
@@ -67,6 +68,8 @@ FLAGS:
-c, --cyclic For periodic reaction coordinates. If this is set, the first and last coordinate bin in each -c, --cyclic For periodic reaction coordinates. If this is set, the first and last coordinate bin in each
dimension are treated as neighbors for the bias calculation. dimension are treated as neighbors for the bias calculation.
-h, --help Prints help information -h, --help Prints help information
-g, --uncorr Estimates statistical inefficiency of each timeseries via autocorrelation and removes correlated
samples (default is off).
-V, --version Prints version information -V, --version Prints version information
-v, --verbose Enables verbose output. -v, --verbose Enables verbose output.
@@ -85,7 +88,6 @@ OPTIONS:
-T, --temperature <temperature> WHAM temperature in Kelvin. -T, --temperature <temperature> WHAM temperature in Kelvin.
-t, --tolerance <TOLERANCE> Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) < -t, --tolerance <TOLERANCE> Abortion criteria for WHAM calculation. WHAM stops if abs(F_new - F_old) <
tolerance (defaults to 0.000001). tolerance (defaults to 0.000001).
``` ```
To run the two dimensional example (simulation of dialanine phi and psi angle): To run the two dimensional example (simulation of dialanine phi and psi angle):
@@ -134,6 +136,18 @@ To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perf
runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a
separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0. separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0.
Autocorrelation analysis
---
With the ```--uncorr``` flag, WHAM calculates the autocorrelation time ```tau``` for all timeseries and all collective
variables. Timeseries are then filtered based on their highest autocorrelation time to remove correlated samples from
the dataset. This reduces the number of data points but can improve the accuracy of the result.
For filtering, the statistical inefficiency `g` is calculated: ```g = 1 + 2*tau```, and only every `g`th element of the
timeseries is used for unbiasing. A more detailed description of the method can be found in
*Chodera, J.D. et al. (2007). Use of the weighted histogram analysis method for the analysis of simulated and parallel
tempering simulations, JCTC 3(1):26-41*
Examples Examples
--- ---
The example folder contains input and output files for two simple test systems: The example folder contains input and output files for two simple test systems: