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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