Update README.md

README.md

@@ -125,6 +125,7 @@ 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 
@@ -168,12 +169,13 @@ python umbrella_integration.py -i infile -o outfile -b binwidth
 	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. 
+    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.
+    written to a folder called derivatives.
+```
 
 
 ----------------------
@@ -216,6 +218,8 @@ umbrella_integration.py
 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"):
@@ -223,6 +227,7 @@ for f in glob.glob("/Documents/PMFsimulations/pdo_*.dat"):
     run_data.append( (f, window_center, fc) )
     ui_input_lines = generate_ui_input_lines_merged(run_data, shift=False)
     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