nvt_prot-dna.mdp

;tittle = Protein-DNA complex NVT equilibration

define = -DPOSRES 				;position restrain the protein and DNA 

; Run parameters 
integrator = md 				;leap-frog integrator 
nsteps = 500000 					;2 * 500000 = 1000 ps 
dt = 0.002 					;2 fs 

; Output control 
nstxout = 500 		;save coordinates every 1.0 ps 
nstvout = 500 		;save velocities every 1.0 ps 
nstenergy = 500 	;save energies every 1.0 ps 
nstlog = 500 		;update log file every 1.0 ps 

; Bond parameters 
continuation = no 				;first dynamics run 
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 

; Neighbour searching and vdW - Nonbonded settings 
cutoff-scheme = Verlet 		;Buffered neighbor searching 
ns_type = grid 				;search neighboring grid cells 
nstlist = 10 				;20 fs, largely irrelevant with Verlet 
rcoulomb = 1.0 				;short-range electrostatic cutoff (in nm) 
rvdw = 1.0 					;short-range van der Waals cutoff (in nm) 
DispCorr = EnerPres 		;account for cut-off vdW scheme 

; 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_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 is off 
pcoupl = no 					;no pressure coupling in NVT 

; Periodic boundary conditions 
pbc = xyz 					;3-D PBC 

; Velocity generation 
gen_vel = yes 					;assign velocities from Maxwell distribution 
gen_temp = 300 					;temperature for Maxwell distribution 
gen_seed = -1 					;generate a random seed