From: Axel Kohlmeyer (
Date: Wed Sep 28 2011 - 09:06:59 CDT

On Wed, Sep 28, 2011 at 7:41 AM, oguz gurbulak <> wrote:
> Dear All,
> I'm trying to compose a tpr file in order to use some gmx 4.5 tools like
> g_rdf, g_order, g_msd, g_hbond. To do it I composed a top file using psf and
> dcd files with topotools1.2 in vmd . Then I used the command
> grompp_d -f min.mdp -c complex.pdb -p -o complex.tpr
> and saw this error:


> ERROR 1 [file, line 18785]:
> ERROR: The cut-off length is longer than half the shortest box vector or
> longer than the smallest box diagonal element. Increase the box size or
> decrease rlist.


> How can I reach this problem ? Could you please help me about this issue ?

first of all, this has _nothing_ to do with topotools.
this is a case of PEBCAC.

your file complex.pdb has no CRYST1 record,
so gromacs has no knowledge of the size of your
simulation cell and hence the error message. it
really helps to read error messages more carefully. ;)

the file complexlastframe.pdb _does_ have it and works.
you may still check out if you have the latest version of
topotools, since i remember having added some improvements
with respect to handling of charge groups recently.

> However, do I need to generate a .ndx file for each gmx analysis tools ?


> make_ndx -f complex.tpr -o complex.ndx ( for example )
> All related files can be downloaded from the link

thanks for providing the files. that made tracking down the issue
and identifying it as a user issue rather than a code issue easy.


> Thank you very much for your attention.
> Kind regards.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.