Update README.md

README.md

@@ -142,29 +142,29 @@ python umbrella_integration.py -i infile -o outfile -b binwidth
     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 
+    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. 
+    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
 -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
 -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
 -o output_pmf_file
@@ -177,7 +177,6 @@ python umbrella_integration.py -i infile -o outfile -b binwidth
     written to a folder called derivatives.
 ```
 
-
 ----------------------
 Format of input file 
 ----------------------
@@ -193,6 +192,7 @@ for the instantaneous value of the the reaction coordinate as a function of
 time). To calculate the PMF the output files for the 10 windows need to be 
 combined into a single file that then contains 10*5000 = 50,000 data points. 
 
+```
 The input file needs to contain the following data in exactly this format:
 
 col 1 = force constant (fc) used in the simulation for that window 
@@ -204,8 +204,10 @@ col 3 = time (that corresponds to the instantaneous value of the reaction
 col 4 = instantaneous value of reaction coordinate at time t in col 3, 
         produced by an umbrella sampling simulation with umbrella at 
         center col 2 and force constant col 1)
+```
+
+For an example see the input files in the test_data folder.
 
-for an example see the input files in the test_data folder.
 
 ----------------------------
 Generating the input file 
@@ -219,7 +221,6 @@ For example, the code below creates an input file using all files of
 format pdo_*.dat in the folder /Documents/PMFsimulations/.
 
 ```
-
 fc = 500.0 # kJ mol-1 nm-2 
 run_data = []
 for f in glob.glob("/Documents/PMFsimulations/pdo_*.dat"):
@@ -229,6 +230,7 @@ for f in glob.glob("/Documents/PMFsimulations/pdo_*.dat"):
     write_output_file("/Documents/PMFsimulations/pdo_merged_ui_input.dat", ui_input_lines)
 ```
 
+```
 To generate the ‘merged’ input file the following data is written:
 col 1 = the force constant, eg. 500 kJ mol-1 nm-2
 col 2 = center of umbrella potential for each data set. taken from the 
@@ -237,6 +239,7 @@ col 2 = center of umbrella potential for each data set. taken from the
 col 3 = time, taken from the input files pdo_*.dat
 col 4 = instantaneous value of reaction coordinate, taken from 
         the input files pdo_*.dat
+```
 
 The merged input file is written to 
 /Documents/PMFsimulations/pdo_merged_ui_input.dat.