md.mdp

title       = Protein-DNA MD simulation

; Run parameters
integrator  = md        ;
nsteps      = 12000000  ; 1 * 12000000 = 12 ns
dt          = 0.001     ; 1 fs

; Output
nstxout             = 1000
nstvout             = 1000
nstenergy           = 1000
nstlog              = 1000
nstxout-compressed  = 1000
compressed-x-grps   = System
energygrps          = Protein DNA

; Bond
continuation    = yes           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type         = grid      ; search neighboring grid cells
nstlist         = 10        ;
rcoulomb        = 1.2       ; short-range electrostatic cutoff
rvdw            = 1.2       ; short-range VdW cutoff

; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT

; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_DNA Water_and_ions    ; 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
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for 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        ; assign velocities from Maxwell distribution