Update README.md

README.md

@@ -9,7 +9,7 @@ Authors: Martin Stroet (University of Queensland)
 When using this program please cite the following paper 
 
 	Deplazes E., Stroet M, Passioura T., Chassagnon I., Cristofori-Armstrong B., 
-	Rash LD., King GF., Mark AE., Journal, vol. no. (year) 
+	King GF., Mark AE., Journal, vol. no. (year) 
 	DOI
 
 Please also cite the GitHub project using the following DOI
@@ -122,4 +122,55 @@ http://matplotlib.org/api/pyplot_api.html
 SciPy 
 https://www.scipy.org/getting-started.html
 
+--------------------
+Running the program
+--------------------
 
+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). 
+-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 
+-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. 
+-m min_max_value
+       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
+-r integration_error_reference
+        Integration error estimation reference point, left or right
+-ie integration_error_method
+	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.
+-t truncate_based_on_convergence
+        remove equilibration (non-converged) region from data set 
+        as determined by convergence analysis method
+-d output_dir
+	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. 
+-w derivatives_file
+	derivative vs time data is written for each bin position, files are 
+        written to a folder called derivatives.