title                    = generic mdp file
cpp                      = /lib/cpp
include                  = -I../top
define                   = 
integrator               = md
dt                       = 0.0001
comm_mode                = None
nsteps                   = 2000000 
nstxout                  = 100
nstvout                  = 100
nstlog                   = 100
nstenergy                = 100
nstxtcout                = 100
xtc_grps                 = system
energygrps               = system
nstlist                  = 10
ns_type                  = grid
;; no periodic boundary condition
pbc                      = full
rlist                    = 1.0
coulombtype              = cut-off
vdwtype                  = cut-off
rcoulomb                 = 1.0
rvdw                     = 1.0
;; 
tcoupl                   = Berendsen
tc-grps                  = system
tau_t                    = 0.1
ref_t                    = 300
Pcoupl                   = no
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = none

# uncomment and change for simulated annealing - check that the sim runs for long enough
;annealing = single
;annealing_npoints = 3
;annealing_time = 0 5 19.5
;annealing_temp = 600 600 0


; uncomment to freeze appropriate stuff
;freezegrps          =  Au1
;comm_grps           =  Au1
;energygrps          =  Au1 AZt
;energygrp_excl          =  Au1 Au1
;freezedim           = Y Y Y