;   template md.mdp for use with OpenMM mdrun
;   November 18, 2008
;   Christopher Bruns
integrator 	= 	sd 
t_init 		= 	0.0
dt 		=	0.002
nsteps 		=	5000
init_step       =       0

energygrps 	= 	system	
; mode for center of mass motion removal
comm-mode                = linear
; number of steps for center of mass motion removal
nstcomm                  = 10
; group(s) for center of mass motion removal
energygrps               = system

; neighbour searching
nstlist 	= 	20000001
nstype 		= 	simple
pbc 		= 	no
rlist 		=  	100	

coulombtype 	= 	cut-off
epsilon_r 	= 	1
rcoulomb 	= 	100

vdwtype 	= 	cut-off
rvdw 		= 	100

; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld_seed                  = 1993
coulombtype 	= 	cut-off
epsilon_r 	= 	1 ; double check this is what we want
rcoulomb 	= 	100

vdwtype 	= 	cut-off
rvdw 		= 	100

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 0 ; zephyr uses to track time
nstenergy                = 0
; Output frequency and precision for xtc file
nstxtcout                = 0
xtc_precision            = 1000

tc-grps 	= 	system
tau_t 		=       0.01099	
; tau_t 		=       1.00
ref_t 		= 	300
gen_vel 	=	yes
gen_temp 	= 	300

; pressure coupling
pcoupl  = no
tau_p   = 0.500
ref_p   = 1.0
compressibility = 4.5e-5

; constraints 	= 	none           
constraints 	= 	hbonds             
constraint_algorithm =	shake 
shake_tol       =       0.00001

implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78.3

; VMD live visualization
; nstvmdout                = 100
; vmdSocketNumber          = 3000
; blockUntilVmdConnected   = 1