;
;	Input file
;
title               =  Octamer			; a string
cpp                 =  /lib/cpp			; c-preprocessor
define              =  -DFLEX_SPC
dt                  =  0.002			; time step
integrator          =  steep 
nsteps              =  4000			; number of steps
nstcomm             =  1			; reset c.o.m. motion
nstxout             =  2000			; write coords
nstvout             =  50			; write velocities
nstlog		    =  50			; print to logfile
nstenergy           =  50			; print energies
energygrps          =  System
nstlist             =  10			; update pairlist
ns_type             =  grid
constraint_algorithm      =  shake
shake_tol           = 0.0001
coulombtype         =  PME
vdwtype             =  shift
rlist               =  1.4			; cut-off for ns
rvdw                =  1.4
rvdw_switch	    =  0.8
rcoulomb            =  1.4
rcoulomb_switch	    =  0.8
tcoupl              =  berendsen		; temperature bath (yes,no)
ref_t		    =  298 
tc_grps             =  Protein 
tau_t		    =  0.1
Pcoupl              =  no
tau_p               =  0.5
ref_p               =  1.0 
gen_vel             =  yes			; generate initial velocities
gen_temp            =  298			; initial temperature
gen_seed            =  173529			; random seed
emtol               =  100
emstep              =  0.01