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

[abhijit Kayal]

Hi,
I have looked at your carbon nanotube coordinate file (arm.gro). There the
terminal C atoms are hydrogen terminated. But you
modified the ffnonbonded.itp file with only C atoms. You need to add the
parameters for H atoms also both in ffnonbonded.itp and
 atomname2type.n2t file. Hope this will work.
Thanks
Abhijit

On Fri, Mar 27, 2015 at 5:17 PM, Hao Ren <renh.cn at gmail.com> wrote:

> 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
> --
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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur