[gmx-users] Error when using AFM Pulling

Bob Johnson robertjo at physics.upenn.edu
Wed Feb 22 20:12:28 CET 2006

Hello everyone,
I'm trying to use AFM pulling. I am entering the following command:

mdrun -s topol.tpr -o pull.trr -c pull.g96 -e pull.edr -g pull.log -pi pull.ppa
-n index.ndx

The .ppa file looks like this:
verbose = no
runtype = afm
group_1 = DA
;group_2 = nanotube
reftype = com
pulldim = N N Y
afm_rate1 = 0.0005
afm_k1 = 1000
reference_group = nanotube

The index file looks like:

[ nanotube]
atom numbers

[ DA ]
atom numbers

However, I get the following message:

Fatal error: No groups in indexfile

I don't understand this message because I have several groups defined in the
index file. What is the problem?

Bob Johnson

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