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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
