[gmx-users] Re: "Re: Segmantation fault at g_traj"

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 13 12:54:15 CEST 2010

Jorge Alberto Jover Galtier wrote:
> Hi, Justin.
> Thank you for answering so quickly. We write you directly because we 
> receive the daily digest from Gromacs and we are not sure how to answer 
> to the thread. We have tried what you suggested, using 10,000 steps and 

Reply to the message, strip out any unnecessary posts in the digest, and change 
the subject line back to what you originally set it as (i.e., not "gmx-users 
digest...").  I must insist that you keep all correspondence on the list so that 
others can benefit from the conversation, and hopefully help out if necessary.

> writing data every 100 steps, and we still have the same problem. The 
> protein we are using is a very small one, with 59 atoms, and we are 
> working in vacuum.

What about my suggestion for using g_traj -b and/or -e to write just a few 
frames?  This would be a far more useful test.

> The only idea we have is that maybe we are making some mistakes at 
> generating the .gro and .top files. These are the instructions we are 
> using. From the .pdb file, we use:

Your problem is from an analysis tool, not from any of these files.  Your 
simulation successfully ran, but your analysis broke down.  The only file worth 
checking would be the .trr file (using gmxcheck), in case it was corrupted 
during the run.

> pdb2gmx -ignh -f pep.pdb -o pep.gro -p pep.top
> We use the default force field and water model. And then we create the 
> box to the protein:
> editconf -f pep.gro -d 0.7 -o pep_ini.gro
> After that, we begin the simulations. We send you the files we are 
> working with, in case you want to try something. And if you have some 

I don't have the means or reason to re-run your system from the start.  As I 
said, the problem is with an analysis tool, not the run itself.

If g_traj is still failing, please post a complete description of your hardware, 
compilers, etc including all of the following:

1. Gromacs version
2. Compilers used (version is especially important)
3. Installation commands (configuration)
4. Hardware and OS


> other ideas, we would be really pleased to read them.
> Thank you very much in advance and best wishes,
> Jorge Alberto Jover Galtier
> Universidad de Zaragoza, Spain
> "Anuncia tu coche Gratis con AutoScout24" 
> <http://addoubleclick.net/clk;227212367;7031886;i?http://www.autoscout24.es/QuickSearch.aspx?extcidm=7628a0308201490>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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