Manually created xtra files in the NAMD or GOMC folders cause a warning.

[bc118]

If the user manually enters extra files in the NAMD or GOMC folders it produces a warning the folder numbers do not match. Maybe add to the warning that the user may have also manually entered files or folders in the directory that are causing errors.

**Code snippet from combining file :(Note: Im sorting by directories, then only comparing '_a" folders .)

namd_directory_a_list = []
total_namd_directory_list = sorted(os.listdir(python_file_directory + '/' + str(path_namd_runs)))
no_total_namd_directory_list = len(total_namd_directory_list)
for i in range(0, len(total_namd_directory_list)):
namd_directory_iter = str(total_namd_directory_list[i])
if namd_directory_iter[-2:] == '_a':
namd_directory_a_list.append(namd_directory_iter)
namd_directory_a_list = sorted(namd_directory_a_list)
no_namd_directory_a = len(namd_directory_a_list)
if no_namd_directory_a != no_total_namd_directory_list:
print("WARNING: The total NAMD directories does not match the '..._a (NAMD liq box)' directories")