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

[Hao Ren]

Thank you Justin for conforming this. /ren

On Fri, Mar 27, 2015 at 9:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/15 7:47 AM, Hao Ren 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?
>>
>>
> There is a bug in the code.  I found the offending commit and will file a
> Redmine issue.  In the meantime, just use an older version to generate the
> topology.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>