GROMACS version: 2021.4

GROMACS modification: Yes/No

Here post your question : I prepared an equilibrated box of cyclohexane. But the desired density was achieved after an NPT equilibration of 20 ns. Is this okay or advisable for so long NPT equilibration? Or am I wrong at some initial step?

npt.mdp is as follows-

title = charmm36 CYHE system NPT equilibration

; Run parameters

integrator = md ; leap-frog integrator

nsteps = 10000000 ; 2 * 10000000 = 20000 ps

dt = 0.002 ; 2 fs

; Output control

nstenergy = 500 ; save energies every 1.0 ps

nstlog = 500 ; update log file every 1.0 ps

nstxout-compressed = 500 ; save coordinates every 1.0 ps

; Bond parameters

continuation = yes ; continuing from NVT

constraint_algorithm = lincs ; holonomic constraints

constraints = h-bonds ; bonds to H are constrained

lincs_iter = 1 ; accuracy of LINCS

lincs_order = 4 ; also related to accuracy

; Neighbor searching and vdW

cutoff-scheme = Verlet

ns_type = grid ; search neighboring grid cells

nstlist = 20 ; largely irrelevant with Verlet

rlist = 1.2

vdwtype = cutoff

vdw-modifier = force-switch

rvdw-switch = 1.0

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

; Electrostatics

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

rcoulomb = 1.2

pme_order = 4 ; cubic interpolation

fourierspacing = 0.16 ; grid spacing for FFT

; Temperature coupling

tcoupl = V-rescale ; modified Berendsen thermostat

tc-grps = system ; two coupling groups - more accurate

tau_t = 1.0 ; time constant, in ps

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

; Pressure coupling

pcoupl = C-rescale ; pressure coupling is on for NPT

pcoupltype = isotropic ; uniform scaling of box vectors

tau_p = 5.0 ; time constant, in ps

ref_p = 1.0 ; reference pressure, in bar

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

refcoord_scaling = com

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction is not used for proteins with the C36 additive FF

DispCorr = no

; Velocity generation

gen_vel = no ; velocity generation off after NVT