;
;	Input file
;
title               =  dock			; a string
cpp                 =  /usr/bin/cpp			; c-preprocessor
dt                  =  0.002			; time step
integrator          =  md
nsteps              =  5000000			; number of steps (1ns)
nstcomm             =  1			; reset c.o.m. motion
nstxout             =  2500			; write coords
nstvout             =  5000			; write velocities
nstfout             =  0  
nstlog		    =  5000			; print to logfile
nstenergy           =  500			; print energies
nstlist             =  10			; update pairlist
; Neighbour Searching
ns_type             = grid			; pairlist method
; Electrostatics and VdW
coulombtype         =  PME
vdwtype             =  Cut-off
rlist               =  1.4			; cut-off for ns
rvdw_switch         =  0.8
rvdw                =  1.4			; cut-off for vdw
rcoulomb_switch     =  0.8
rcoulomb            =  1.4			; cut-off for coulomb
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
;Temperature coupling
Tcoupl              =  berendsen			; temperature bath (yes,no)
ref_t		    =  300        300
tc-grps		    =  Protein  Non-Protein
tau_t		    =  0.1        0.1
; Pressure coupling
Pcoupl              =  berendsen
pcoupltype          =  isotropic
; pressure bath
tau_p               =  0.5
compressibility     =  4.575e-4
ref_p               =  1.0
energygrps          =  protein  sol  UNK   Na
; Velocity generation
gen_vel             =  yes			; generate initial
gen_temp            =  300.0			; initial temperature
gen_seed            =  173529			; random seed
constraints         =  all-bonds
constraint-algorithm  = shake
unconstrained-start   = yes
comm_grps           =  Protein  Non-Protein
comm_mode           =  Linear ; added to remove translation