[gmx-users] error while running mdrun

[ananyachatterjee]

 Dear all,

 While running mdrun using following mdpparameters:

 title        = Model MD
 ; Run parameters
 integrator    = md
 nsteps        = 5000000
 dt        = 0.002
 ; Output control
 nstxout        = 500
 nstvout        = 500
 nstxtcout    = 500
 nstenergy    = 500
 nstlog        = 500
 nstcomm         = 100
 ; Bond parameters
 continuation    = yes
 constraint_algorithm = lincs
 constraints    = none
 lincs_iter    = 1
 lincs_order    = 4
 ns_type        = grid
 nstlist        = 5
 rlist        = 0.9
 rcoulomb    = 0.9
 rvdw        = 1.4
 ; Electrostatics
 coulombtype    = PME
 pme_order    = 4
 fourierspacing    = 0.15
 optimize_fft    = yes
 ; Temperature coupling is on
 tcoupl        = V-rescale
 tc-grps        = Protein Non-Protein
 tau_t        = 0.5    0.5
 ref_t        = 300     300
 ; Pressure coupling is on
 pcoupl        = Parrinello-Rahman
 pcoupltype    = isotropic
 tau_p        = 2.0
 ref_p        = 1.0
 compressibility = 4.5e-5
 ; Periodic boundary conditions
 pbc        = xyz        ; 3-D PBC
 ; Dispersion correction
 DispCorr    = EnerPres
 ; Velocity generation
 gen_vel        = yes


 Using multiple processor and I got this following error,

 t = 239.934 ps: Water molecule starting at atom 75561 can not be 
 settled.
 Check for bad contacts and/or reduce the timestep.
 Wrote pdb files with previous and current coordinates
 [ganga:04205] *** Process received signal ***
 [ganga:04205] Signal: Segmentation fault (11)
 [ganga:04205] Signal code: Address not mapped (1)
 [ganga:04205] Failing at address: 0x201a01c20
 [ganga:04204] *** Process received signal ***
 [ganga:04205] [ 0] /lib/libpthread.so.0(+0xfb40) [0x7fa773ac5b40]
 [ganga:04205] [ 1] /usr/lib/libmd_mpi_openmpi.so.5(+0x73064) 
 [0x7fa774749064]
 [ganga:04205] [ 2] /usr/lib/libmd_mpi_openmpi.so.5(gmx_pme_do+0x323) 
 [0x7fa77474f420]
 [ganga:04205] [ 3] /usr/lib/libmd_mpi_openmpi.so.5(gmx_pmeonly+0x1be) 
 [0x7fa77474f095]
 [ganga:04205] [ 4] mdrun_mpi(mdrunner+0x13df) [0x416f1d]
 [ganga:04205] [ 5] mdrun_mpi(main+0x797) [0x41c862]
 [ganga:04205] [ 6] /lib/libc.so.6(__libc_start_main+0xfe) 
 [0x7fa773750d8e]
 [ganga:04205] [ 7] mdrun_mpi() [0x4056d9]
 [ganga:04205] *** End of error message ***
 [ganga:04204] Signal: Segmentation fault (11)
 [ganga:04204] Signal code: Address not mapped (1)
 [ganga:04204] Failing at address: 0x7518df0
 --------------------------------------------------------------------------
 mpirun noticed that process rank 10 with PID 4205 on node ganga exited 
 on signal 11 (Segmentation fault).
 --------------------------------------------------------------------------
 [ganga:04204] [ 0] /lib/libpthread.so.0(+0xfb40) [0x7f488c4e3b40]
 [ganga:04204] [ 1] /usr/lib/libgmx_mpi_openmpi.so.5(+0x10db29) 
 [0x7f488cd2fb29]
 [ganga:04204] *** End of error message ***
 mani at ganga:~/project/gromacs/MUT$


 Can any one help me where I am getting wrong.
-- 
 Ananya Chatterjee,
 Senior Research Fellow (SRF),
 Department of biological Science,
 IISER-Kolkata.