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

[abhijit Kayal]

If the earlier versions generate the topology then I guess the problem is
in your installation.
I can't help you much in this regard cause I never tried g_x2top in gromacs
5 version.

Thanks
 Abhijit

On Fri, Mar 27, 2015 at 6:11 PM, Hao Ren <renh.cn at gmail.com> wrote:

> 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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-- 
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur