[gmx-users] problem with -select flag in gmx distance

[Irem Altan]

Hi,

I am trying to follow Justin’s umbrella sampling tutorial, and I ran into a problem while calculating the CoM distance between two chains. The command I’m trying to run is:

gmx_mpi distance -s pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg -select 'com of group "Chain_A" plus com of group "Chain_B”'

which results in the following error:

Program:     gmx distance, VERSION 5.1.2
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:    void gmx::CommandLineParser::parse(int *, char **)

Error in user input:
Invalid command-line options
  In command-line option -select
    Invalid selection 'com'
      While parsing 'com'
        'of' is missing
  In command-line option -select
    Invalid selection 'group'
      Near 'group'
        syntax error
  In command-line option -select
    Invalid selection 'plus'
      Near 'plus'
        syntax error
  In command-line option -select
    Invalid selection 'com'
      While parsing 'com'
        'of' is missing
  In command-line option -select
    Invalid selection 'group'
      Near 'group'
        syntax error

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Halting program gmx distance

However, if I remove the part after the -select flag, and interactively enter the same string, it works. What might be the problem?

Best,
Irem