Hi,
I'm having a problem with mdrun seg-faulting after ~240 ps of
unrestrained simulation. I'm using 3.3.1 on a beowulf cluster.
Below are the tails of the output files. I've also listed the .mdp
at the end.
I've tried varying some of the parameters(dt and tau_p), but the
simulations always seem to run to about 200 ps before crashing. How
can I find out more information about what's going on here? The EM
(run to machine convergence) and PR (100 ps) always run fine. It
seems to me that if it was an equilibration problem, it'd happen
before running for so long.
Thanks for any help!
Jim Fonseca
*log from parallel node 0*
Step Time Lambda
120000 240.00000 0.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.067432 7188 7189 0.005393
After LINCS 0.000131 8250 8253 0.000021
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. Improper
Dih. LJ-14
7.02762e+04 2.34867e+04 2.53603e+04 7.54128e+03
2.46027e+04
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
Potential
1.54268e+05 2.16502e+05 -2.96632e+06 -6.02749e+05
-3.04703e+06
Kinetic En. Total Energy Temperature Pressure (bar)
5.09231e+05 -2.53780e+06 2.99996e+02 3.08941e+01
*output redirect fom mdrun*
^Mstep 120180, will finish at Wed Jun 28 13:04:09 2006
^Mstep 120190, will finish at Wed Jun 28 13:04:13 2006
^Mstep 120200, will finish at Wed Jun 28 13:04:17 2006
Back Off! I just backed up step120205.pdb to ./#step120205.pdb.1#
Back Off! I just backed up step120206.pdb to ./#step120206.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step120206.pdb to ./#step120206.pdb.2#
Back Off! I just backed up step120206.pdb to ./#step120206.pdb.3#
Back Off! I just backed up step120207.pdb to ./#step120207.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step120207.pdb to ./#step120207.pdb.2#
Back Off! I just backed up step120207.pdb to ./#step120207.pdb.3#
Back Off! I just backed up step120207.pdb to ./#step120207.pdb.4#
Back Off! I just backed up step120208.pdb to ./#step120208.pdb.1#
Back Off! I just backed up step120208.pdb to ./#step120208.pdb.2#
Back Off! I just backed up step120208.pdb to ./#step120208.pdb.3#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
mpiexec: Warning: tasks 7-13 died with signal 11 (Segmentation fault).
*full.mdp*
title = 2agv_full
cpp = /usr/bin/cpp
;include = -I../top
;define = -DPROPOSRES -DLIPPOSRES
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 500000 ;1000 ps
nstxout = 10000
nstvout = 10000
nstlog = 10000
nstenergy = 1000
nstxtcout = 1000
xtc_grps = Protein SOL POP Na
energygrps = Protein SOL POP Na
nstlist = 10
ns_type = grid
rlist = 1.4
coulombtype = PME
rcoulomb = 1.4
rvdw = 1.4
tcoupl = Berendsen
tc-grps = Protein SOL POP Na
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
Pcoupl = Berendsen
pcoupltype = anisotropic
tau_p = 1.00
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p = 1.0 1.0 1.0 0.0 0.0 0.0
gen_vel = yes
gen_temp = 300
gen_seed = -1
optimize_fft = yes
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