[gmx-users] memory usage grows without bounds

[Pablo Serra]

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