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

[Justin Lemkul]

On 10/27/16 9:51 AM, Irem Altan wrote:
> 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?
>

Works for me.  Are you having problems with the scripted version, or one that 
you're invoking yourself?  If the latter, be sure your use of single and double 
quotes is correct.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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