[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x

[Hao Ren]

Hi there,


I am trying a MD simulation for carbon nanotubes, but encountered a problem
in the preparation of topology file.

The coordinates and modified force filed can be found here:
https://www.dropbox.com/s/qv4j33sivn56iey/test_x2top.tgz?dl=0

I prepared the modified OPLS/AA force filed as described earlier in this
list, post by Dr. Abhijit Kayal (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090353.html
).

A topology file can be generated by the g_x2top module from gromacs 4.0.7
and 4.6.7 using the command line:

g_x2top -f arm.gro -o topol.top -ff cnt_oplsaa


However, I got a segmentation fault for gromacs 5.0.x, when I use the
following command:

gmx x2top -f arm.gro -o topol.top -ff cnt_oplsaa

I have tried several OS/gcc combinations (centos 6.5/gcc-4.8.2,
centos7/gcc-4.8.2, centos6.5/gcc-4.4.7, OSX10.9/homebrew-gcc-4.9.2) with
fftw-3.3.4/gcc-4.8.2, all terminated with seg fault.

I am not sure whether it comes from my invalid modification of force field
or inappropriate compilation of gromacs or an internal bug of the gromacs
code.

Could anyone kindly help me to locate this problem? Or just test whether
you can reproduce the error using your gromacs 5.0.x installation?

I appreciate any help and suggestion,

Best Regards,

/ren



PS: The STDOUT looks like the following,
=============
GROMACS:      gmx x2top, VERSION 5.0.4
Executable:   /opt/gromacs/5.0.4/bin/gmx
Library dir:  /opt/gromacs/5.0.4/share/gromacs/top
Command line:
  gmx x2top -f arm.gro -o top.top -ff cnt_oplsaa

Opening force field file ./cnt_oplsaa.ff/atomname2type.n2t
There are 26 name to type translations in file ./cnt_oplsaa.ff
Generating bonds from distances...
atom 560
There are 3 different atom types in your sample
Generating angles and dihedrals from bonds...
Segmentation fault (core dumped)
==============

--

Hao Ren, Ph. D.

Center for Bioengineering & Biotechnology

China University of Petroleum

Huangdao, Qingdao, Shandong 266580, P. R. China

Email: renh at upc.edu.cn

Tel: +86-(532) 8698 1135

http://pme.upc.edu.cn/~ren