I have run a 100ns simulation run of my protein, but I would like to know about the initial atomic velocity that is assigned. Below is the md.mdp file that was available from the GROMACS tutorial provided by Lemkul which I have used for my simulation run.

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title = protein

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns)

dt = 0.002 ; 2 fs

; Output control

nstxout = 0 ; suppress bulky .trr file by specifying

nstvout = 0 ; 0 for output frequency of nstxout,

nstfout = 0 ; nstvout, and nstfout

nstenergy = 5000 ; save energies every 10.0 ps

nstlog = 5000 ; update log file every 10.0 ps

nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps

compressed-x-grps = System ; save the whole system

; Bond parameters

continuation = yes ; Restarting after NPT

constraint_algorithm = lincs ; holonomic constraints

constraints = h-bonds ; bonds involving H are constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighborsearching

cutoff-scheme = Verlet ; Buffered neighbor searching

ns_type = grid ; search neighboring grid cells

nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme

rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)

rvdw = 1.0 ; 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 ; modified Berendsen thermostat

tc-grps = Protein Non-Protein ; two coupling groups - more accurate

tau_t = 0.1 0.1 ; time constant, in ps

ref_t = 300 300 ; reference temperature, one for each group, in K

; Pressure coupling is on

pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT

pcoupltype = isotropic ; uniform scaling of box vectors

tau_p = 2.0 ; time constant, in ps

ref_p = 1.0 ; reference pressure, in bar

compressibility = 4.5e-5 ; isothermal compressibility of water, 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

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