[gmx-users] Crashing NPT run, 1.5 ns
JMandumpal
jesbman at rediffmail.com
Wed May 28 14:22:43 CEST 2008
Dear list,
I was running AA acetone in tip4p water simulation for calculating average density : NPT for 1.5 ns, but, after 600 ps the simulation crashes . I came to know from older posts, this may result with an inappropriate value of P-couple. I increased the value from 0.4, which was using before, to 5.0, still the simulation crashes. I paste the error message, the input file for the simulation and the parameter file for acetone. Could you please point out where I did make mistake.
regards,
Jestin
*************************************************
Error message from a program output file:
****************************************************
Reading file binary.tpr, VERSION 3.3.3 (double precision)
starting mdrun 'Pure water - acetone'
750000 steps, 1500.0 ps.
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step281955.pdb to ./#step281955.pdb.1#
Wrote pdb files with previous and current coordinates
MPI: On host cognac, Program /opt/gromacs/3.3.3/bin/mdrun, Rank 2, Process 2410 received signal SIGSEGV(11)
MPI: --------stack traceback-------
sh: idb: command not found
MPI: -----stack traceback ends-----
MPI: On host cognac, Program /opt/gromacs/3.3.3/bin/mdrun, Rank 2, Process 2410: Dumping core on signal SIGSEGV(11) into directory /short/bm01/jestin/acetone/40/180
MPI: MPI_COMM_WORLD rank 2 has terminated without calling MPI_Finalize()
MPI: aborting job
****************************************************************
my input file (.mdp file):
------------------------------------------------------
title = ACETONE
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
dt = 0.002 ; 2 fs
nsteps = 750000 ; 1500ps
; For exact run continuation or redoing part of a run
init_step = 0
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps = system
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 0
nstvout = 0
nstfout = 0
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 0
nstenergy = 10000
; Output frequency and precision for xtc file
nstxtcout = 0
xtc-precision = 1000
; select multiple groups. By default all atoms will be written.
; NEIGHBORSEARCHING PARAMETERS
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions:
pbc = xyz
; nblist cut-off
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb = 1.0
ewald_rtol = 1.0e-5 ; since erfc(sigma*rcutoff)=ewald_rtol
optimize_fft = yes
; Relative dielectric constant for the medium
epsilon_r = 1 ; for water
; Method for doing Van der Waals
vdw-type = cut-off
rvdw = 1.0
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_geometry = 3d
epsilon_surface = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = system
; Time constant (ps) and reference temperature (K)
tau-t = 0.1
ref-t = 180
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 5.0
compressibility = 4.5e-5
ref-p = 1.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen-temp = 180
gen-seed = 173529
constraints = all-bonds
constraint_algorithm = shake
shake_tol = 0.0001
morse = no
**********************************************************************
acetone parameter file:
----------------------------------------------
[ moleculetype ]
; Name nrexcl JPC 94, 1685
ACET 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 opls_280 1 ACET C_2 1 0.470 12.0110
2 opls_281 1 ACET O_2 1 -0.470 15.9994
3 opls_135 1 ACET CT1 2 -0.180 12.0110
4 opls_282 1 ACET HC1 2 0.060 1.00800
5 opls_282 1 ACET HC2 2 0.060 1.00800
6 opls_282 1 ACET HC3 2 0.060 1.00800
7 opls_135 1 ACET CT2 3 -0.180 12.0110
8 opls_282 1 ACET HC4 3 0.060 1.00800
9 opls_282 1 ACET HC5 3 0.060 1.00800
10 opls_282 1 ACET HC6 3 0.060 1.00800
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.12290 476976.0 ; C_2 O_2 ketone group
3 1 1 0.15220 265265.6 ; C_2 CT1 methylcarbon - keto carbon
7 1 1 0.15220 265265.6 ; C_2 CT1 methylcarbon - keto carbon
3 4 1 0.10900 284512.0 ; CT1 HC1 methylC- hydrogen
3 5 1 0.10900 284512.0 ; CT1 HC2 methylC- hydrogen
3 6 1 0.10900 284512.0 ; CT1 HC3 methylC- hydrogen
7 8 1 0.10900 284512.0 ; CT2 HC4 methylC- hydrogen
7 9 1 0.10900 284512.0 ; CT2 HC5 methylC- hydrogen
7 10 1 0.10900 284512.0 ; CT2 HC6 methylC- hydrogen
[ angles ]
; ai aj ak fu c0, c1, ...
3 1 7 1 116.00 585.760 ; CT1 C_2 CT2
3 1 2 1 120.40 669.440 ; CT1 C_2 O_2
4 3 1 1 109.50 292.880 ; HC1 CT1 C_2
5 3 1 1 109.50 292.880 ; HC1 CT1 C_2
7 1 2 1 120.40 669.440 ; CT2 C_2 0_2
8 7 1 1 109.50 292.880 ; HC4 CT2 C_2
9 7 1 1 109.50 292.880 ; HC4 CT2 C_2
10 7 1 1 109.50 292.880 ; HC4 CT2 C_2
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
7 1 3 4 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone
7 1 3 5 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone
7 1 3 6 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone
3 1 7 8 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone
3 1 7 8 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone
3 1 7 8 3 0.57530 1.72590 0.00000 -2.30120 0.00000 0.00000 ; ketone
4 3 1 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
5 3 1 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
6 3 1 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
8 7 1 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
9 7 1 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
10 7 1 2 3 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
3 7 1 2 3 3.10662 -3.77606 -5.13795 5.80739 0.00000 0.00000 ; ketone improper dihedral
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