In the tutorial the goal was to provide an equilibrated system for the next step. If you want a “production” run or not depends on what the goal of this simulation is. If there is anything you would like to study you can probably do that during the final 10 ns simulation, but discarding the samples until the system is stable (using the -b <time> option in gmx energy). I don’t think you will need a separate production simulation.
Ok. Got this. For my study, after building the biphasic system, I need to center my protein in the system, then go for the subsequent steps of MD simulation.
After NVT equilibration of 500 ps on the cyclohexane box, still I am getting unstable system-
nvt.mdp parameters are as follows-
title = charmm36 CYHE NVT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000 ; 2 * 250000 = 500 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 = no ; first dynamics run
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 ; short-range electrostatic cutoff (in nm)
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 = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = no ; no pressure coupling in NVT
; 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 = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
I am using charmm36 ff and the box is cubic (4.9 nm) with 218 cyclohexane molecules in it. Can you please tell me how much more equilibration needed so that my system can be stable?