Update README.md

README.md

@@ -131,50 +131,50 @@ python umbrella_integration.py -i infile -o outfile -b binwidth
 -w writeDerivatives -c convergenceCheck -p plotPmf 
 
 -i infile 
-	name of input file, if file is not in the same directory as 
-    the script, the full path needs to be given. (see below for details on
-    the format of the input file). 
+   name of input file, if file is not in the same directory as 
+   the script, the full path needs to be given. (see below for details on
+   the format of the input file). 
 -b bin_width
-	the bin width used for 'binning derivatives' when calculating the PMF 
-    (ie when combining the data from the different windows). 
-    if -b is not given, the default of 0.2 (nm) is used. 
-    This is independent of the spacing between umbrellas/windows used 
-    in the umbrella sampling simulations. 
-    NOTE: the bin widths affects the final PMF so this 
-	should be carefully considered (see also Kästner & Thiel 2005). 
-    Instead of the bin_width -n and -m can be used to provide 
-    the number of binds and the range (min,max) for the 
-    reaction coordinate 
+   the bin width used for 'binning derivatives' when calculating the PMF 
+   (ie when combining the data from the different windows). 
+   if -b is not given, the default of 0.2 (nm) is used. 
+   This is independent of the spacing between umbrellas/windows used 
+   in the umbrella sampling simulations. 
+   NOTE: the bin widths affects the final PMF so this 
+   should be carefully considered (see also Kästner & Thiel 2005). 
+   Instead of the bin_width -n and -m can be used to provide 
+   the number of binds and the range (min,max) for the 
+   reaction coordinate 
 -n number_bins
-	Number of bins to be used along the reaction coordinate. This is 
-    independent of the umbrellas/windows used in umbrella sampling 
-    simulations. 
+   Number of bins to be used along the reaction coordinate. This is 
+   independent of the umbrellas/windows used in umbrella sampling 
+   simulations. 
 -m min_max_value
-    Minimum and maximum reaction coordinate positions to be considered 
-    e.g. -m 0.2 5.5
+   Minimum and maximum reaction coordinate positions to be considered 
+   e.g. -m 0.2 5.5
 -p show_plots
-	if yes, the final PMF is plotted as an image. default=false
+   if yes, the final PMF is plotted as an image. default=false
 -r integration_error_reference
-    Integration error estimation reference point, left or right
+   Integration error estimation reference point, left or right
 -ie integration_error_method
-	Method for propagating integration errors
+    Method for propagating integration errors
 -c run_convergence
-    convergence analysis on the data set at each umbrella 
-    equilibrium position is run using the script runAnalysis.py        
-    in the folder convergence_analysis.
+   convergence analysis on the data set at each umbrella 
+   equilibrium position is run using the script runAnalysis.py        
+   in the folder convergence_analysis.
 -t truncate_based_on_convergence
-    remove equilibration (non-converged) region from data set 
-    as determined by convergence analysis method
+   remove equilibration (non-converged) region from data set 
+   as determined by convergence analysis method
 -d output_dir
-	Output directory for window convergence analysis plots
+   Output directory for window convergence analysis plots
 -o output_pmf_file
-	Name of output file that contains the final PMF.
-    Format, col 1 = reaction coordinate, col 2 = energy.
-    if error analysis is  included, col 3 = uncertainty
-    if option -o is not given, default name pmf.dat is used. 
+   Name of output file that contains the final PMF.
+   Format, col 1 = reaction coordinate, col 2 = energy.
+   if error analysis is  included, col 3 = uncertainty
+   if option -o is not given, default name pmf.dat is used. 
 -w derivatives_file
-	derivative vs time data is written for each bin position, files are 
-    written to a folder called derivatives.
+   derivative vs time data is written for each bin position, files are 
+   written to a folder called derivatives.
 ```
 
 ----------------------
@@ -327,6 +327,7 @@ the input -t can be used to truncate the data used for the
 calculation of the final PMF. Alternatively, the following global 
 variables can be used to control whether 
 non-converged data is used for the calculation of the final PMF. 
+
 ```
 TRUNCATE_DATA_BASED_ON_CONVERGENCE_ANALYSIS = True
 If true, the data set for a given window is truncated and only the converged
@@ -355,10 +356,33 @@ perhaps).
 Test data / Examples
 ----------------------
 
-The folder test_data contains input data for three types of umbrella sampling 
-simluations
+The folder test_data contains data from three types of umbrella sampling 
+simulations:
+- peptide binding to a protein
+  reaction coordinate = peptide-protein distance (COM)
+- peptide binding to a lipid bilayer
+  reaction coordinate = peptide-bilayer distance (COM)
+- Na ion binding to a lipid bilayer
+  reaction coordinate = ion-bilayer distance (COM)
+
+The following are examples of how to run umbrella integration on the 
+peptide-protein system. the file protein_system_merged_ui_input.dat contains 
+the combined data from umbrella sampling simulations using 120 windows 
+(10,000 data points per window) with 31 different equilibrium positions
+ranging from 3.45 to 6.85
+
+to calculate the PMF without convergence analysis, using 50 bins 
+from 3.2 to 6.9, integration error from left, final pmf is written 
+to pmfUI.dat. writes out the derivatives for each bin (not the umbrella
+positions) to a file called derivatives.dat
 
+```
+python umbrella_integration.py -i test_data/protein_system/protein_system_merged_ui_input.dat -n 50 -m 3.2 6.9 -r left -o test_data/protein_system/pmfUI.dat -p -w test_data/protein_system/derivatives.dat 
+```
+
+to include convergence analysis 
+```
+python umbrella_integration.py -i test_data/protein_system/protein_system_merged_ui_input.dat -n 50 -m 3.2 6.9 -r left -o test_data/protein_system/pmfUI.dat -p -w test_data/protein_system/derivatives.dat -c 
 
-python umbrella_integration.py -i /Users/e.deplazes/Desktop/MD/ASIC1a/PMF/3S3X/analysis_new/0to10ns_UI/pdo_new_windows_all_windows_0to10ns_merged.dat -n 50 -m 3.2 6.9 -r left -o /Users/e.deplazes/Desktop/MD/ASIC1a/PMF/3S3X/analysis_new/0to10ns_UI/pmfUI_ASIC1aPcTx1_newwindows_0to10ns.dat
+ ```
 
-