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

[Wolfram Stacklies]

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
http://www.picb.ac.cn/graeter/files_wolfram/tube.pdb

There are also little extras for x2top to run correctly on the nanotube:
http://www.picb.ac.cn/graeter/files_wolfram/ffgmxbon.itp
http://www.picb.ac.cn/graeter/files_wolfram/ffencadv.n2t

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
using
8: Encad all-atom force field, using scaled-down vacuum charges
(the bug also happens when trying to use OPLS)

Best regards,
Wolfram