; Run parameters
integrator	= md	        ; leap-frog integrator
nsteps		= 100000000 	; 200 ns
dt		= 0.002		; 2 fs

; mode for center of mass motion removal
comm-mode                = Linear

; Output control
nstxout		= 0		; save coordinates every 0.2 ps
nstvout		= 0		; save velocities every 0.2 ps
nstenergy	= 0		; save energies every 0.2 ps
nstlog		= 0		; update log file every 0.2 ps
xtc_grps        = 
energygrps      = 
nstxtcout       = 100

ns_type		= grid		; search neighboring grid cells
nstlist		= 5		; 10 fs
rlist		= 1		; short-range neighborlist cutoff (in nm)
rcoulomb	= 1		; short-range electrostatic cutoff (in nm)
rvdw		= 1		; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype	= PME	; Particle Mesh Ewald for long-range electrostatics
pme_order	= 4		; cubic interpolation
fourierspacing	= 0.15		; grid spacing for FFT
ewald_rtol      = 1e-05
optimize_fft    = yes

; Temperature coupling is on
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
pbc		= xyz		; 3-D PBC

; Method for doing Van der Waals
vdw-type        = Cut-off

gen_vel		= no		; assign velocities from Maxwell distribution

; OPTIONS FOR BONDS    
continuation             = 
constraints              = all-bonds
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = Ener
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 30

; Non-equilibrium MD stuff
freezegrps               = 
freezedim                = 

; Electric fields      
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x                      = 
E-xt                     = 
E-y                      = 
E-yt                     = 
E-z                      = 1 0.000001 0 ;  v/nm ;10 v/cm
E-zt                     =