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