[gmx-users] Using groups in the mdp file

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 6 19:06:40 CET 2012

francesco oteri wrote:
> 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.

In principle, an index file is not necessary here, as ACX should be generated as 
a default group since it is defined as a [moleculetype].


Perhaps the OP can provide the original grompp command and whether or not the -n 
flag was invoked.  An incorrect index file can also give this error, I believe, 
if it does not contain the desired group.

>> energy_grps          = ACX

This is an incorrect keyword that should have raised a fatal error.  The proper 
keyword is "energygrps."



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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