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

[吴鹏]

Dear All:

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

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.

Questions:
1. I speculate that the segmentation fault is caused by thread
conflict, i.e., I somehow break parallelization in Gromacs - is this
right?
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,

Peng