[gmx-users] Problem with system minimization

[Lum Nforbi]

Hello all,

I am minimizing a system of 2000 water molecules again but I have several
error messages. Is my timestep too large indeed? The error message also
mentions segmentation fault. I have only 6000 atoms in my system but the
output shows atom 7783 and 8879. I'm not sure what's going on. My pdb file
is shown below and the output of the minimization is written after the
output.
Please, help me locate the problem.

; VARIOUS PREPROCESSING OPTIONS
title                    = NPT simulation of water
cpp                      = /lib/cpp
include                  = -I../top
define                   =

; RUN CONTROL PARAMETERS
integrator               = steep
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.002
nsteps                   = 5000
simulation_part          = 1
init_step                = 0
comm-mode                = Linear
nstcomm                  = 1

; LANGEVIN DYNAMICS
bd-fric                  = 0
ld-seed                  = 1993

; ENERGY MINIMIZATION OPTIONS
emtol                    = 1000
emstep                   = 0.01

; OUTPUT CONTROL OPTIONS
nstxout                  = 500
nstvout                  = 500
nstfout                  = 0
nstlog                   = 500
nstenergy                = 500
nstxtcout                = 100
xtc-precision            = 1000
xtc-grps                 = SOL
energygrps               = SOL
;
; PARAMETERS FOR NEIGHBORSEARCHING
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
periodic_molecules       = no
rlist                    = 0.9

; ELECTROSTATICS AND VDW OPTIONS
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.9
vdw-type                 = Cut-off
rvdw                     = 1.4
DispCorr                 = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.135
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes


t = 4.066 ps: Water molecule starting at atom 1993 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step= 2034, Dmax= 3.4e-02 nm, Epot=  1.48017e+09 Fmax= 1.08293e+08, atom=
7783
Step= 2035, Dmax= 4.0e-02 nm, Epot=  1.46516e+09 Fmax= 1.83787e+09, atom=
1993
Step= 2037, Dmax= 2.4e-02 nm, Epot=  1.44351e+09 Fmax= 2.34469e+08, atom=
1993
Step= 2038, Dmax= 2.9e-02 nm, Epot=  1.42904e+09 Fmax= 4.29069e+08, atom=
1993
Step= 2039, Dmax= 3.5e-02 nm, Epot=  1.41457e+09 Fmax= 2.10114e+08, atom=
1993
Step= 2040, Dmax= 4.2e-02 nm, Epot=  1.39993e+09 Fmax= 3.01888e+08, atom=
1993
Step= 2042, Dmax= 2.5e-02 nm, Epot=  1.38636e+09 Fmax= 2.28092e+08, atom=
4549
Step= 2043, Dmax= 3.0e-02 nm, Epot=  1.37259e+09 Fmax= 1.40258e+08, atom=
4549
Step= 2044, Dmax= 3.6e-02 nm, Epot=  1.35660e+09 Fmax= 4.77136e+08, atom=
4549
Step= 2045, Dmax= 4.3e-02 nm, Epot=  1.34145e+09 Fmax= 1.32867e+08, atom=
4549
Step= 2047, Dmax= 2.6e-02 nm, Epot=  1.32970e+09 Fmax= 3.61866e+08, atom=
3097
Step= 2048, Dmax= 3.1e-02 nm, Epot=  1.31958e+09 Fmax= 3.14277e+08, atom=
3097
Step= 2049, Dmax= 3.7e-02 nm, Epot=  1.31567e+09 Fmax= 9.12713e+08, atom=
3964
Step= 2050, Dmax= 4.5e-02 nm, Epot=  1.30841e+09 Fmax= 6.21777e+08, atom=
3964
Step= 2051, Dmax= 5.4e-02 nm, Epot=  1.30480e+09 Fmax= 5.82421e+08, atom=
3637

t = 4.104 ps: Water molecule starting at atom 3637 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step= 2052, Dmax= 6.5e-02 nm, Epot=  1.29311e+09 Fmax= 4.72304e+08, atom=
3079

t = 4.106 ps: Water molecule starting at atom 3079 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Step= 2054, Dmax= 3.9e-02 nm, Epot=  1.27930e+09 Fmax= 1.93571e+08, atom=
8879
Step= 2056, Dmax= 2.3e-02 nm, Epot=  1.26788e+09 Fmax= 3.64079e+08, atom=
1411
Step= 2057, Dmax= 2.8e-02 nm, Epot=  1.25869e+09 Fmax= 2.08411e+08, atom=
5857
Step= 2058, Dmax= 3.4e-02 nm, Epot=  1.24544e+09 Fmax= 1.25967e+08, atom=
5857
Step= 2060, Dmax= 2.0e-02 nm, Epot=  1.23279e+09 Fmax= 1.91600e+08, atom=
1411
Step= 2061, Dmax= 2.4e-02 nm, Epot=  1.22254e+09 Fmax= 1.33277e+08, atom= 88
Step= 2062, Dmax= 2.9e-02 nm, Epot=  1.20834e+09 Fmax= 1.80612e+08, atom=
1411
Step= 2063, Dmax= 3.5e-02 nm, Epot=  1.20371e+09 Fmax= 4.86526e+08, atom=
1411
Step= 2064, Dmax= 4.2e-02 nm, Epot=  1.20033e+09 Fmax= 8.14034e+08, atom=
5857
Step= 2065, Dmax= 5.0e-02 nm, Epot=  1.18726e+09 Fmax= 3.57392e+08, atom=
2851
Step= 2067, Dmax= 3.0e-02 nm, Epot=  1.18000e+09 Fmax= 3.11047e+08, atom=
2851
Step= 2068, Dmax= 3.6e-02 nm, Epot=  1.17184e+09 Fmax= 3.86104e+08, atom=
4048
Step= 2069, Dmax= 4.3e-02 nm, Epot=  1.16512e+09 Fmax= 3.59701e+08, atom=
4162
Step= 2070, Dmax= 5.2e-02 nm, Epot=  1.15932e+09 Fmax= 3.93044e+08, atom=
4162
Step= 2072, Dmax= 3.1e-02 nm, Epot=  1.14698e+09 Fmax= 6.99317e+07, atom=
2236
Step= 2073, Dmax= 3.7e-02 nm, Epot=  1.13498e+09 Fmax= 5.46620e+08, atom=
2236
Step= 2074, Dmax= 4.5e-02 nm, Epot=  1.11948e+09 Fmax= 5.85052e+08, atom=
4825
Step= 2075, Dmax= 5.4e-02 nm, Epot=  1.10614e+09 Fmax= 2.05211e+08, atom=
4162

t = 4.152 ps: Water molecule starting at atom 4162 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault

Thank you,
Lum
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