[gmx-users] Umbrella sampling-gmx distance

[Justin Lemkul]

On 1/11/18 11:38 AM, rose rahmani wrote:
>   [ ZnS ]
>     1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
>    16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>    31   32   33   34   35   36   37   38   39   40   41   42   43   44
>   45..............
>
> [ Protein ]
>   761  762  763  764  765  766  767  768  769  770  771  772  773  774  775
>   776  777  778  779  780  781  782  783  784  785  786
>
> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group "ZnS"
> plus com of group "Protein"' -oxyz -oall
> i exactly select index groups!!!
> -------------------------------------------------------
> Program:     gmx distance, VERSION 5.1.4
> Source file: src/gromacs/selection/selectioncollection.cpp (line 616)
> Function:    void gmx::SelectionCollection::setI
> ndexGroups(gmx_ana_indexgrps_t*)
>
> Inconsistency in user input:
> Invalid index group reference(s)
>    Cannot match 'group "ZnS"', because no such index group can be found.
>    Cannot match 'group "Protein"', because no such index group can be found.
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ------------------------------------------------------------
> ---------------------------------
> so i had to use this command;  gmx distance -n index.ndx -f conf0.gro
> -select -oxyz
> GROMACS:      gmx distance, VERSION 5.1.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>    gmx distance -n index.ndx -f conf0.gro -select -oxyz
>
> Available static index groups:
>   Group  0 "System" (4336 atoms)
>   Group  1 "Other" (760 atoms)
>   Group  2 "ZnS" (560 atoms)
>   Group  3 "WAL" (200 atoms)
>   Group  4 "NA" (5 atoms)
>   Group  5 "CL" (5 atoms)
>   Group  6 "Protein" (26 atoms)
>   Group  7 "Protein-H" (12 atoms)
> .
> .
> (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end)
>> 2
> Selection '2' parsed
>> 6
> Selection '6' parsed

You should be selecting 'com of group 2' etc. here to get what you want. 
I don't know why the command-line version of this didn't work, but to 
get a COM distance, you need to tell gmx distance to do it, otherwise 
it's just going to produce pairwise distances, which is what you're 
asking for here.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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