[gmx-users] Using groups in the mdp file

Ignacio Fernández Galván jellby at yahoo.com
Mon Feb 6 17:26:13 CET 2012

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?


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