[gmx-users] time steps and segmentation fault

albitauro at virgilio.it albitauro at virgilio.it
Mon Oct 19 15:29:55 CEST 2009

 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)
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,


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