[gmx-developers] Bug in x2top, gromacs-4.0.5

Wolfram Stacklies wolfram.stacklies at gmail.com
Mon Jul 13 08:05:56 CEST 2009

Hello Everybody,

I guess I found a bug in x2top. I was trying to generate a topology
for a carbon nanotube, what works fine with the x2top coming with
gromacs-3.3.x. If I try to run with the gromacs-4.0.5 x2top instead
the program will hang for days, running at 100% cpu but showing no
progress at all.
Looking at the source code, there are quite a lot of changes between
the two versions, so I can't really tell what's causing the problem.

The pdb file used to generate the topology can be found under

There are also little extras for x2top to run correctly on the nanotube:

The procedure is also described on http://cs86.com/index.html

And the command was:
x2top -f tube.pdb -o tube.top -r tube.rtp -ff select
8: Encad all-atom force field, using scaled-down vacuum charges
(the bug also happens when trying to use OPLS)

Best regards,

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