[gmx-users] time steps and segmentation fault

[XAvier Periole]

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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