define               	 =  -DPOSRES

integrator           	 =  md
dt                   	 =  0.002	; ps !
nsteps               	 =  50000	; total 100ps.

; OPTIONS FOR BONDS
; Constrain control
constraints	         =  all-bonds
; Do not constrain the start configuration
continuation      = no
; Type of constraint algorithm
constraint-algorithm     =  lincs

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                 =  100000
nstvout              	 =  100000
nstfout              	 =  100000
; Output frequency and precision for xtc file
nstxtcout           	 =  5000
xtc-precision        	 =  1000
; Energy monitoring
energygrps           	 =  Protein	Non-protein	
nstenergy	         =  5000

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist              	 =  5 
; ns algorithm (simple or grid)
ns-type              	 =  Grid
; nblist cut-off        
rlist                	 =  0.8

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = Reaction-Field  
rcoulomb 		            = 1.4 
epsilon_rf		         = 62    ; As suggested at J Comput Chem. 2004 Oct;25(13):1656-76.
vdw-type                 = Cut-off
; cut-off lengths       
rvdw                     = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl                   = berendsen
; Groups to couple separately, time constant (ps) and reference temperature (K)
tc-grps                  = Protein     Non-Protein
tau-t                    = 0.1	       0.1
ref-t                    = 300	       300
; Pressure coupling     
Pcoupl                   = berendsen
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    =  1.0 
compressibility          =  4.5e-5      
ref_p                    =  1.0
; Generate velocites is on at 290K - do not get velocity from gro file.
gen_vel             =  yes
gen_temp            =  290
gen-seed            =  -1



; Center of mass control
nstcomm              =  1000
; Periodic boundary conditions 
pbc                  =  xyz
; Mode for center of mass motion removal
comm-mode            =  Linear
; Groups for center of mass motion removal
comm-grps            =  system