[gmx-users] Re: Persistent crashes due to unsettled waters

Aaron Fafarman aarontf at stanford.edu
Mon Nov 3 00:31:08 CET 2008

Thanks for the tip about the "blowing-up" page on the wiki--I already
checked there and found little help because my crashes are coming so
long into the runs (sometimes as late as 1 million steps in). This is
also why I can't debug with nstxout = 1: the output files would get
too big. I'm also reluctant to lower the time-step from 2 fs to say 1
fs, because I'm already resource-limited in these simulations, and
slowing them down would halve the amount of sampling I could do.

Any other thoughts on this?

The mdp file for these crashing runs is shown below:

integrator      = md
nsteps          = 2000000
dt              = 0.002
nstlist         = 10
nstcomm         = 1
rlist           = 1.0
coulombtype     = pme
rcoulomb        = 1.0
vdw-type        = cut-off
rvdw            = 1.0
tcoupl          = Nose-Hoover
tc-grps         = protein non-protein
tau-t           = 0.5 0.5
ref-t           = 298 298
nstxout         = 1000
nstxtcout       = 100
nstenergy       = 100

> Message: 7
> Date: Fri, 31 Oct 2008 20:43:22 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Persistent crashes due to unsettled waters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <490BA62A.8000007 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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:
> http://wiki.gromacs.org/index.php/blowing_up
> 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.
> -Justin

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