[gmx-users] Water molecules cannot be settled, why?

John Ladasky blind.watchmaker at yahoo.com
Mon Jun 4 21:53:25 CEST 2012

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) 
[j-l:02837] [ 1] /usr/lib/libgmx_mpi.openmpi.so.6(+0x1da5a1) 
[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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