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@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
--
========================================
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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