[gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

吴鹏 gerogewu8 at gmail.com
Mon Oct 4 18:23:22 CEST 2010

Dear All:

I am trying to do trajectory analysis on-the-fly and encountered some

What did I do:
I inserted a small piece of code into "md.c" to READ the position of
atoms and do some simple analysis. In the GMX3.2, my code works fine.

The problem:
In GMX4.5.1, my code works only if I set mdrun -nt to 1, i.e. force GMX
to use one thread. Otherwise, mdrun reports segmentation fault.

1. I speculate that the segmentation fault is caused by thread
conflict, i.e., I somehow break parallelization in Gromacs - is this
2. Is it possible to perform on-fly analysis or other types of
customization of Gromacs when multi-threading is enabled?
3. If answer to 2 is yes, where can I find the documentations for
doing so, and how difficult is it to write multi-threading code using
Gromacs's own library?

Thank you very much for your time.

Best regards,


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