old_contents: __author__ = 'vivek'
  
  '''
  
  Purpose :   This file merges the results of the simulation stage into one
              coordinate file as is required by the LSDMap analysis stage.
              This file reads from the simulation CU outputs and writes them
              into one common file in linear order.
  
  Arguments : num_CUs = number of compute units
              md_output_file = name of the resulting output file
              path = path of the corresponding compute unit to read from
  
  '''
  
  import os
  import sys
  
  if __name__ == '__main__':
      num_CUs = int(sys.argv[1])
      md_output_file = sys.argv[2]
      path = sys.argv[3]
  
      with open(md_output_file, 'w') as output_grofile:
          for i in range(0,num_CUs):
              with open('%s/out%s.gro' % (path,i), 'r') as output_file:
                  for line in output_file:
                      print >> output_grofile, line.replace("\n", "")
                      
      os.system('echo 2 | trjconv -f tmp.gro -s tmp.gro -o tmpha.gro')
  
new_contents: __author__ = 'vivek'
  
  '''
  
  Purpose :   This file merges the results of the simulation stage into one
              coordinate file as is required by the LSDMap analysis stage.
              This file reads from the simulation CU outputs and writes them
              into one common file in linear order.
  
  Arguments : num_CUs = number of compute units
              md_output_file = name of the resulting output file
              path = path of the corresponding compute unit to read from
  
  '''
  
  import os
  import sys
  
  if __name__ == '__main__':
      num_CUs = int(sys.argv[1])
      md_output_file = sys.argv[2]
      path = sys.argv[3]
  
      with open(md_output_file, 'w') as output_grofile:
          for i in range(0,num_CUs):
              with open('%s/out%s.gro' % (path,i), 'r') as output_file:
                  for line in output_file:
                      print >> output_grofile, line.replace("\n", "")
                      
      os.system('echo 2 | gmx trjconv -f tmp.gro -s tmp.gro -o tmpha.gro')
  
subject: update for gromacs 5.1*