Recently I have started to get crash messages in my molecular dynamics
runs which look like this:
Reading file exp37b-prep.tpr, VERSION 4.5.4 (single precision)
Making 1D domain decomposition 5 x 1 x 1
starting mdrun 'Protein in water'
500000 steps, 1000.0 ps.
step 81240: Water molecule starting at atom 45191 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
[j-l:02837] *** Process received signal ***
[j-l:02837] Signal: Segmentation fault (11)
[j-l:02837] Signal code: Address not mapped (1)
[j-l:02837] Failing at address: 0x422112b0
[j-l:02837] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10060)
[0x7fb79a50d060]
[j-l:02837] [ 1] /usr/lib/libgmx_mpi.openmpi.so.6(+0x1da5a1)
[0x7fb79aba55a1]
[j-l:02837] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 4 with PID 2837 on node j-l exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
The surprising thing to me is that I'm getting the water molecule
settling error after a very large number of simulation steps. As you
can see, this occurred on step 81,240. In another related simulation,
it takes over 100,000 steps before an error occurs. Any time that I
have set up a simulation incorrectly in the past, I always get an error
quickly, usually a LINCS error.
If I rerun the exact same simulation, the problem is reproducible. My
current project compares four conformations of a partially-folded
protein. Only two of these four conformations produce a water settling
error within the time frame I am testing (500,000 steps, representing
1.0 ns of real time).
Recently I have been trying to avoid the -deuterate option in pdb2gmx,
thinking that I might be introducing biases into my simulations by using
it. However, am I correct in thinking that the -deuterate option does
not affect the hydrogen atoms of the solvent that I add using genbox and
spc216.gro? So, switching back to using -deuterate should not affect
the motion of solvent hydrogens, at least, not directly.
I would appreciate any guidance you may have. Thanks!
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