[gmx-users] Problems with using AFM Pulling

Berk Hess gmx3 at hotmail.com
Fri Dec 2 14:08:17 CET 2005

>From: Bob Johnson <robertjo at physics.upenn.edu>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: GROMACS Mailing List <gmx-users at gromacs.org>
>Subject: [gmx-users] Problems with using AFM Pulling
>Date: Thu, 01 Dec 2005 20:49:27 -0500
>Hello everyone,
>I'm trying to use the AFM pulling feature in Gromacs. However, every time I 
>mdrun I get the following error:
>Groups: 5P
>Pull code using absolute reference.
>Using 1 pull groups
>Using distance components 0 0 1
>Back Off! I just backed up pull.pdo to ./#pull.pdo.1#
>Fatal error: Can't find group  in the index file
>In my index file I have the following:
>[ 5P ]
>   32
>Along with additional groups not used in the pull. I don't understand why 
>can't find the 5P group that I defined. Does anyone know what's wrong?

The problem is not that it can not find the group 5P.
In the error message there are two spaces between "group" and "in",
so it seems that mdrun thinks the name of the pull group is an empty string.
You can look in pullout.ppa, generated by mdrun, to see if there are any
hints to what might have caused the empty string.


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