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

[Hao Ren]

Thank you for your prompt reply, Abhijit.

I removed all the hydrogen atoms in arm.gro, and changed the number of
atoms from 560 to 520, then run the command

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

and, unfortunately, segmentation fault again.

It seems that in previous versions (4.6.7 and 4.0.7), g_x2top recognises
the hydrogen atoms in the coordinate file (arm.gro) as opls_140:
==
H    opls_140    0.06    1.008  1    C 0.108
==
has a single bond with a carbon atom with length 0.108.

So I think the seg fault is probably not caused by the hydrogen atoms,
(though the using of opls_140 seems problematic ...)

/ren


--

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

On Fri, Mar 27, 2015 at 8:27 PM, abhijit Kayal <abhijitchemiitd at gmail.com>
wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
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>
>
> --
> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
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