[gmx-users] Re: Segmentation fault, mdrun_mpi

[Ladasky]

Bumping this once before the weekend, hoping to get some help.

I am getting segmentation fault errors at 1 to 2 million cycles into my
production MD runs, using GROMACS 4.5.4.  If these errors are a consequence
of a poorly-equilibrated system, I am no longer getting the right kind of
error messages to support that conclusion.  I am not getting PME or SETTLE
errors.  I am getting a non-descriptive segmentation fault.

I have corrected earlier shortcomings in my equilibration protocols, as
discussed in this earlier thread:

http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-tp4999302.html

I am now monitoring the macroscopic properties of my simulation.  Potential,
pressure, density, and temperature convergence and subsequent stability are
achieved, at least as well as demonstrated in Justin Lemkul's most recent
tutorial:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

The trajectories of my simulations do not appear to be radical in any way
that I can discern.  I have a partially-unfolded protein, folding gradually,
in a box of water with counter-ions.

>From my previous thread, I have come to appreciate just how far from
equilibrium the initial state of a simulation can be.  Also, I have always
understood that MD simulations are chaotic, and that instabilities can
result simply from the fact that a continuous system is being modeled in
discrete time steps.  (As an aside, one of my first programming puzzles was
about exactly this kind of thing.  When I was a high-school student, I
wanted to simulate the orbits of the Moon about the Earth, and the Earth
about the Sun.  It sounded simple enough, just apply the inverse-square law
for gravity, right?  Yet no matter how I tried, I couldn't achieve a stable
system.  Deeper reading led me to the intuitive and quick "leapfrog" method
of improving differential approximations, which GROMACS apparently uses: and
the more powerful but slower Runge-Kutta methods, which GROMACS apparently
does not use.)

By correcting my earlier problems, I have extended the time that my
simulations will run by a factor of 10-20 fold, out to several nanoseconds. 
That's progress, but I'm never going to get to one microsecond this way.

Any advice is appreciated.  Of course I can post MDP files again, as well as
graphs.




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