[gmx-users] x2top segmentation fault in gromacs 5.0.x, but runs well for 4.0.x, 4.6.x
Hao Ren
renh.cn at gmail.com
Fri Mar 27 14:05:15 CET 2015
I just used the topology file generated by g_x2top 4.6.7 to solvate the
system with my 5.0.4 installation
==
gmx solvate -cp arm.gro -p top.top -o arm_solvated.gro
==
and succeed.
I also succeed in several test simulations, such as Dr. Lemkul's tutorials
I, II and III using my 5.0.4 installation.
But even I can not say this seg fault comes from my compilation or from the
updated x2top module in the 5.0.x release.
Thanks Abhijit anyway.
ren
On Fri, Mar 27, 2015 at 8:49 PM, abhijit Kayal <abhijitchemiitd at gmail.com>
wrote:
> 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
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> Gromacs Users mailing list
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