[gmx-users] syntax for gmx distance

[Teemu Murtola]

The error message really looks like that your shell does not understand the
quoting. You need to pass the whole selection as a single command-line
parameter (which your quotes in principle would do), but the error message
indicates that each word is getting parsed as a separate selection, so your
shell is passing them as separate arguments.

Best regards,
Teemu

On Mon, Sep 14, 2015, 11:28 Nash, Anthony <a.nash at ucl.ac.uk> wrote:

Dear all,

I understand that this is quite a basic question, but I think I need a
fresh set of eyes to figure out what¹s going on with gmx distance -select
syntax.

In my index file, I have 23 groups, two of which are ³ZINC² and ³CARBONYL²

Based on numerous mail archive suggestions and the gromacs website change
in tools page, I¹m using:

$CHEM/rungromacs505 gmx distance -n index.ndx -f umb_1_all.trr -s
umb_1_umb.tpr -oh umb_1_distance_hist.xvg -oall umb_1_distance.xvg -select
'com of group "ZINC" plus com of group "CARBONYL"'

Which kicks up the error:

Invalid command-line options
  In command-line option -select
    In keyword 'com'
      required parameter 'of' not specified
    invalid selection 'com'
  In command-line option -select
    syntax error
    invalid selection 'group'
  In command-line option -select
    syntax error
    invalid selection 'plus'
  In command-line option -select
    In keyword 'com'
      required parameter 'of' not specified
    invalid selection 'com'
  In command-line option -select
    syntax error
    invalid selection 'group'

I¹d appreciate any suggestions. I¹ve also tried to do *something* via the
interactive command line (when -select is not supplied), but what it¹s
asking for is a bit cryptic.

Thanks
Anthony