fep_long.mdp

integrator               = sd
dt                       = 0.002
nsteps                   = 6000000
nstxout                  = 5000
nstvout                  = 5000
nstlog                   = 5000
nstenergy                = 250
;nstxout-compressed       = 250
rlist                    = 1.0
coulombtype              = PME
pme_order                = 6
fourierspacing = 0.1
cutoff-scheme   = Verlet
ns_type = grid        ; search neighboring grid cells
nstlist    = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb                 = 1.0
rvdw                     = 1.0
; and pressure to 1 bar
pcoupl = parrinello-rahman
ref-p = 1
compressibility = 4.5e-5
tau-p = 5 
gen-vel                  = $GEN_VEL$
gen-temp                 = 300
gen-seed                 = 173529
constraints              = hbonds
constraint_algorithm =  lincs
lincs-order =  12
tc_grps             =  System
tau_t               =  1.0 
ld_seed             =  -1
ref_t = 298.15 

; Free energy
free_energy = yes
init-lambda-state = $STATE$
calc-lambda-neighbors = -1
sc_alpha = 0.0
couple-lambda1 = vdw-q
fep-lambdas = $ALL_LAMBDAS$
coul-lambdas = $ALL_LAMBDAS$
vdw-lambdas = $ALL_LAMBDAS$
DispCorr = EnerPres