[gmx-users] Persistent crashes due to unsettled waters

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 1 01:43:22 CET 2008

Aaron Fafarman wrote:
> Dear GMX-community,
> I'm running four related, equilibrium-dynamics simulations of a small
> protein in explicit water, each with a different non-natural
> amino-acid in the sequence. One of the four non-natural amino-acid
> containing proteins can be simulated for long times, up to 4 ns
> without incident, but the other three invariably crash. On repeated
> reinitialization (changing the box size, changing the duration of
> position restrained refinement) they still keep crashing at any time
> between 100's of picoseconds and 2 ns. Usually an error such as
> "3009.270 ps: Water molecule starting at atom 26883 can not be
> settled." is printed to the log file and the pdb of the step after the
> crash has nonsense numbers for the coordinates of the offending water
> molecule. It's always a different water molecule, always a
> high-numbered atom (>20000). The crashes happen on both a
> self-compiled linux build and on a self-compiled Mac OS 10.4 build,
> both GMX 3.3.1.  A simulation of just the parameterized amino acids in
> a box of water never crashes over the course of a 4 ns simulation so I
> don't suspect my amino-acid parameters.

As a general reference, check out the following:


For debugging purposes, I have found that if I set nstxout = 1 in the .mdp file, 
I can usually capture the initial events leading to the explosion. 
Unfortunately, the water molecule that cannot be settled is usually an 
unfortunate victim of another molecule that has gone flying off across your system.

It might also be useful to post your .mdp file here if you are still unable to 
find the problem.


>  I'm using ffamber99 and I parameterized the amino acids myself using
> antechamber and amb2gmx. I'm using ffamber_tip3p. Thanks for reading.
> -Aaron
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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