[gmx-users] Gromacs 2018.3 Exceeding Memory Issue

[Peiyin Lee]

Hi, all GROMACS users,

   I am trying to run jobs with Gromacs 2018.3 version and constantly got a
memory exceeding error. The system I ran is an all-atom system with 21073
atoms. The largest file that is estimated to be generated is around 5.8 GB.
My jobs got constantly killed after running for only around 15 minutes and
got an error message like this: "slurmstepd: error: Job 12381762 exceeded
memory limit (123122052 > 122880000), being killed". I have tried using a
larger memory specification (12GB/core) but it would take too long to wait
and I don't think my job really uses that many memories. I have attached my
.mdp file as below:
"title = NVT Production Run for Trpzip4 in pure H2O

define =        ; position restrain the protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 50000000 ; 0.002 * 50000 = 100000 ps (100 ns)

dt     = 0.002 ; 2 fs

; Output control

nstenergy = 10000 ; save energies every 20 ps

nstlog = 10000 ; update log file every 20 ps

nstxout-compressed = 10000      ; 20ps

compressed-x-precision = 200   ; 0.05

compressed-x-grps       = System

; Bond parameters

continuation = yes     ; Restarting after NVT

constraint_algorithm = lincs ; holonomic constraints

constraints = all-bonds         ; all bonds (even heavy atom-H bonds)
constrained

lincs_iter = 1             ; accuracy of LINCS

lincs_order = 4             ; also related to accuracy

; Neighborsearching

ns_type = grid ; search neighboring grid cels

nstlist = 5     ; 10 fs

rlist = 1.2 ; short-range neighborlist cutoff (in nm)

rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)

rvdw = 1.2 ; short-range van der Waals cutoff (in nm)

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics

pme_order = 4     ; cubic interpolation

fourierspacing = 0.16 ; grid spacing for FFT

; Temperature coupling is on

tcoupl = V-rescale         ; More accurate thermostat

tc-grps = Protein SOL NA        ; 2 coupling groups - more accurate

tau_t = 0.5 0.5 0.5        ; time constant, in ps

ref_t = 400 400  400     ; reference temperature, one for each group, in K

; Pressure coupling is on

pcoupl = No      ; Pressure coupling on in NPT

pcoupltype = isotropic     ; uniform scaling of x-y box vectors,
independent z

tau_p = 5.0         ; time constant, in ps

ref_p = 1.0         ; reference pressure, x-y, z (in bar)

compressibility = 4.5e-5 ; isothermal compressibility, bar^-1

; Periodic boundary conditions

pbc     = xyz ; 3-D PBC

; Dispersion correction

DispCorr = EnerPres ; account for cut-off vdW scheme

; Velocity generation
gen_vel = no ; Velocity generation is off"
and the command I used to run was "mpirun -np 80 gmx_mpi mdrun -npme 16
-noappend -s md.tpr -c md.gro -e md.edr -x md.xtc -cpi md.cpt -cpo md.cpt
-g md.log". This is my first time posting so please excuse anything that's
unclear. I will try to clarify if needed. Any help is greatly appreciated!

Regards,
Peiyin Lee