[gmx-users] time steps and segmentation fault

albitauro at virgilio.it albitauro at virgilio.it
Thu Oct 22 11:54:16 CEST 2009

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.
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?

Thank you for your help.


----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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