[gmx-users] Using groups in the mdp file

[francesco oteri]

Hi Ignacio,
You can solve the problem creating an index file through make_ndx. In
such a file you need a group called ACX. Then use the index.ndx in
grompp.

Francesco

2012/2/6, Ignacio Fernández Galván <jellby at yahoo.com>:
> Hi all,
>
> I have a system with a molecule called ACX plus water (molecules called
> SOL), but when I try to use "ACX" as a group name in the .mdp file, grompp
> says such a group does not exist:
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: readir.c, line: 1320
>
> Fatal error:
> Group ACX not found in index file.
> Group names must match either [moleculetype] names
> or custom index group names,in which case you
> must supply an index file to the '-n' option of grompp.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> However, the .top file is, I believe, correct, it contains these lines:
>
> [ moleculetype ]
> ; Name            nrexcl
> ACX               3
>
> and then [atoms], [bonds], etc. It ends with:
>
> [ molecules ]
> ; Compound        #mols
> ACX                 1
> SOL              2139
>
> and that's not a problem. It's when I try to use ACX as a group name, as in:
>
> energy_grps          = ACX
>
> that I get the error. What am I doing wrong? Is there any option I must
> activate to enable using molecule names as groups?
>
> Thanks,
> Ignacio
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-- 
Cordiali saluti, Dr.Oteri Francesco