[gmx-users] error while running mdrun

[Justin Lemkul]

On 12/17/12 5:57 AM, ananyachatterjee wrote:
>
> 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.

Probably insufficient energy minimization.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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