title                    = Alanine dipeptide in water
;Preprocessor
cpp                      = /lib/cpp
;Directories to include in the topology format
;include                 = -I../top
;Run control: A leap-frog algorithm for integrating Newton's equations. 
integrator               = md
;Total simulation time: 100 ps
:time step in femtoseconds 
dt                       = 0.002
;number of steps
nsteps                   = 1000
;frequency to write coordinates to output trajectory file
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
;frequency to write energies to log file
nstlog                   = 100
;frequency to write energies to energy file
nstenergy                = 100
;frequency to write coordinates to xtc trajectory 
nstxtcout                = 100
;group(s) to write to xtc trajectory
xtc_grps                 = System
;group(s) to write to energy file 
energygrps               = Protein non-Protein
;Frequency to update the neighbor list (and the long-range forces, 
;when using twin-range cut-off's). 
nstlist                  = 10
;Make a grid in the box and only check atoms in neighboring grid cells 
;when constructing a new neighbor list every nstlist steps. 
ns_type                  = grid
;cut-off distance for the short-range neighbor list
;treatment of electrostatic interactions
coulombtype = PME 
;treatment of van der waals interactions
rvdw = 1.0 
rlist = 1.0
rcoulomb = 1.0 
cutoff-scheme=Verlet
; Periodic boudary conditions in all the directions 
pbc                      = xyz
;Temperature coupling
tcoupl                   = v-rescale
tc-grps                  = Protein non-Protein
tau_t                    = 0.1 0.1
ref_t                    = 300 300
;Velocity generation
gen_vel                  = yes 
gen_temp                 = 300
gen_seed                 = 173529
;Constrain all bonds
constraints              = all-bonds
