http://www.mdtutorials.com/gmx/lysozyme/Files/md.mdp

title                   = OPLS Lysozyme NPT equilibration ; Run parametersintegrator              = md        ; leap-frog integratornsteps                  = 500000    ; 2 * 500000 = 1000 ps (1 ns)dt                      = 0.002     ; 2 fs; Output controlnstxout                 = 0         ; suppress bulky .trr file by specifying nstvout                 = 0         ; 0 for output frequency of nstxout,nstfout                 = 0         ; nstvout, and nstfoutnstenergy               = 5000      ; save energies every 10.0 psnstlog                  = 5000      ; update log file every 10.0 psnstxout-compressed      = 5000      ; save compressed coordinates every 10.0 pscompressed-x-grps       = System    ; save the whole system; Bond parameterscontinuation            = yes       ; Restarting after NPT constraint_algorithm    = lincs     ; holonomic constraints constraints             = h-bonds   ; bonds involving H are constrainedlincs_iter              = 1         ; accuracy of LINCSlincs_order             = 4         ; also related to accuracy; Neighborsearchingcutoff-scheme           = Verlet    ; Buffered neighbor searchingns_type                 = grid      ; search neighboring grid cellsnstlist                 = 10        ; 20 fs, largely irrelevant with Verlet schemercoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype             = PME       ; Particle Mesh Ewald for long-range electrostaticspme_order               = 4         ; cubic interpolationfourierspacing          = 0.16      ; grid spacing for FFT; Temperature coupling is ontcoupl                  = V-rescale             ; modified Berendsen thermostattc-grps                 = Protein Non-Protein   ; two coupling groups - more accuratetau_t                   = 0.1     0.1           ; time constant, in psref_t                   = 300     300           ; reference temperature, one for each group, in K; Pressure coupling is onpcoupl                  = Parrinello-Rahman     ; Pressure coupling on in NPTpcoupltype              = isotropic             ; uniform scaling of box vectorstau_p                   = 2.0                   ; time constant, in psref_p                   = 1.0                   ; reference pressure, in barcompressibility         = 4.5e-5                ; isothermal compressibility of water, bar^-1; Periodic boundary conditionspbc                     = xyz       ; 3-D PBC; Dispersion correctionDispCorr                = EnerPres  ; account for cut-off vdW scheme; Velocity generationgen_vel                 = no        ; Velocity generation is off

; Run parametersintegrator              = md        ; leap-frog integratornsteps                  = 500000    ; 2 * 500000 = 1000 ps (1 ns)dt                      = 0.002     ; 2 fs

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr

Estimate for the relative computational load of the PME mesh part: 0.22

gmx mdrun -deffnm md_0_1

Command line:  gmx mdrun -deffnm md_0_1

Reading file md_0_1.tpr, VERSION 2020.7 (single precision)Changing nstlist from 10 to 50, rlist from 1 to 1.116
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 12 OpenMP threads
starting mdrun 'LYSOZYME in water'500000 steps,   1000.0 ps.