Dear users,
I'm running a NVT simulation with gromacs 4.5.5,using
the command:
mdrun -nt $NSLOTS
and the memory usage grows without bounds until a crash with the message
/opt/gridengine/default/spool/compute-0-8/job_scripts/1711: line 29: 25200
Killed /usr/local/bin/mdrun -nt $NSLOTS
I've got the same result in several machines with 4, 6 and 8 cores, and
ram between 4 to 23 G. Attached is the memory map of one of a typical run.
I'm running a system of 512 CBrCL_3 molecules (2560 atoms) using the shake
algorithm for the constrains.
The options in the mdp file are:
constraints = all-bonds
integrator = md
dt = 0.005
nsteps = 10000000000
ns_type = grid
nstxtcout = 1000
xtc-precision = 1000
nstxout = 0
nstvout = 0
nstfout = 0
rlist = 1.6
coulombtype = Cut-off
rcoulomb = 1.6
vdw-type = Cut-off
rvdw = 1.6
DispCorr = EnerPres
Tcoupl = Nose-Hoover
tc-grps = System
tau_t = 2.0
ref_t = 180
Pcoupl = no
gen_vel = no ;yes
gen_temp = 180
gen_seed = 1993
; Type of constraint algorithm
constraint-algorithm = shake
shake-tol = 0.0001
Thanks,
Pablo
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