[gmx-users] time steps and segmentation fault

[XAvier Periole]

On Oct 22, 2009, at 11:54 AM, albitauro at virgilio.it wrote:

> Hi,
> I'm checking my system and topology but I noticed a quite weird  
> behaviour in
> this concern.
> When I run my simulation starting from a pre-optimized geometry, the  
> simulation
> crashes with segmentation fault.
what do you mean by pre-optimization?
> On the other hand, when I run the same simulation but starting from  
> the
> geometry I generated "a priori" (without a first step of  
> equilibration) the
> simulation starts and ends correctly. The results look physically  
> correct.
> This is quite disappointing for me since I would expect problems when
> pre-equilibration is missing and not when it is carried out as a  
> preliminar step.
> Furthermore, I find the same behaviour also for similar systems  
> (different dimensions or shapes).
> Maybe more experienced user found already the same behaviour or have  
> an explanation.
> Anyway, do you think that this could be due to some kind of error in  
> the
> topology/input or could my system be just quite critical to be  
> modeled?
Well, it does not make sense, as you noted!
It is difficult to say or interpret your observations as you miss to  
explain
your protocol and type of system.
>
> Thank you for your help.
>
> Alb
>
> ----Messaggio originale----
> Da: x.periole at rug.nl
> Data: 19-ott-2009 2.04 PM
> A: "albitauro at virgilio.it"<albitauro at virgilio.it>, "Discussion list  
> for GROMACS users"<gmx-users at gromacs.org>
> Ogg: Re: [gmx-users] time steps and segmentation fault
>
>
> The type of system you are simulating and the manner you prepared
> are probably responsible for the crash ...
> You should have a good look at it!
>
>
> On Oct 19, 2009, at 3:29 PM, albitauro at virgilio.it wrote:
>
> >  Hi all,
> >
> > I carried out a MD simulation using the MARTINI CG force field and I
> > had some
> > problems.  The simulation stops immediately, reporting a
> > segmentation fault:
> >
> > **********************************************+
> > Making 1D domain decomposition 2 x 1 x 1
> > starting mdrun 'FIB'
> > 200000 steps,   6000.0 ps.
> > step 0
> > [beta:06822] *** Process received signal ***
> > [beta:06822] Signal: Segmentation fault (11)
> > [beta:06822] Signal code: Address not mapped (1)
> > [beta:06822] Failing at address: 0x34321d0
> > [beta:06822] [ 0] /lib/libpthread.so.0 [0x7f7e49b38a80]
> > [beta:06822] [ 1] mdrun_mpi [0x66549a]
> > [beta:06822] *** End of error message ***
> > mpirun noticed that job rank 0 with PID 6822 on node beta exited on
> > signal 11 (Segmentation fault).
> > 1 process killed (possibly by Open MPI)
> > **************************************************
> >
> > I have no WARNINGs in the output of the simulation.
> > However, before, when running grommp I received 1 warning and 1  
> note:
> >
> > ********************************************************
> > WARNING 1 [file aminoacids.dat, line 1]:
> >   For proper thermostat integration tau_t (0.1) should be more  
> than an
> >   order of magnitude larger than delta_t (0.03)
> > ********************************************************
> > and
> > ********************************************************
> > NOTE 1 [file ny6.mdp, line unknown]:
> >   The Berendsen thermostat does not generate the correct kinetic
> > energy
> >   distribution. You might want to consider using the V-rescale
> > thermostat.
> > ********************************************************
> >
> > I used a time step of 0.03 ps and a tau_t of 0.1 (suggested by the
> > authors of MARTINI ff even when using a
> > delta_t=0.04 ps). In any case, modifying the tau_t and avoiding the
> > WARNING does not solve
> > the problem.
> >
> > The simulation starts and ends correctly if I use a delta_t=0.01
> > ps.  However,
> > this time step is not recommended for use with MARTINI ff because
> > the range of
> > time steps used for parametrization is 20-40 fs.
> > Does anyone have any suggestion to solve the problem?
> >
> > Many thanks,
> >
> > AM
> >
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>
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