[gmx-users] segmentation fault.

[sreelakshmi ramesh]

dear gmx-users,
                         During equilibriation i get the following error.Any
suggestions please.

*grompp*

WARNING 1 [file npt.mdp]:
  The sum of the two largest charge group radii (2.369582) is larger than
  rlist (1.000000)


This run will generate roughly 73 Mb of data

There was 1 warning

Back Off! I just backed up npt.tpr to ./#npt.tpr.5#

gcq#113: "I Don't Like Dirt" (The Breeders)

*
mdrun*

WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the
forces deviate on average -2147483648% from minus the numerical derivative
of the potential


WARNING: For the 1498 non-zero entries for table 2 in table_Na_Cl.xvg the
forces deviate on average -2147483648% from minus the numerical derivative
of the potential

Making 1D domain decomposition 2 x 1 x 1

Back Off! I just backed up npt.trr to ./#npt.trr.6#

Back Off! I just backed up ener.edr to ./#ener.edr.23#
starting mdrun 'NA SODIUM ION in water'
50000 steps,     50.0 ps.

step 0: Water molecule starting at atom 6153 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0b_n1.pdb to ./#step0b_n1.pdb.23#

step 0: Water molecule starting at atom 4410 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step0b_n0.pdb to ./#step0b_n0.pdb.23#

Back Off! I just backed up step0c_n1.pdb to ./#step0c_n1.pdb.23#

Back Off! I just backed up step0c_n0.pdb to ./#step0c_n0.pdb.23#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
*Segmentation fault*

*mdp file*
title           = nacl
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000         ; 2 * 50000 = 100 ps
dt              = 0.001         ; 2 fs
; Output control
nstxout         = 100           ; save coordinates every 0.2 ps
nstvout         = 100           ; save velocities every 0.2 ps
nstenergy       = 100           ; save energies every 0.2 ps
nstlog          = 100           ; update log file every 0.2 ps
; Bond parameters
continuation    = no            ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 5             ; 10 fs
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics

coulombtype = user
energygrps = Na Cl Sol
energygrp_table = Na Cl
vdwtype= user

fourierspacing  = 0.16          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = SOL Na Cl     ; two coupling groups - more accurate
tau_t           = 0.1   0.1 0.1 ; time constant, in ps
ref_t           = 300   300 300 ; reference temperature, one for each group,
in K
; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC


; Velocity generation
gen_vel= yes
gen_temp= 300.0
gen_seed= -1
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