Lista de parâmetros para uma simulação no GROMACS (versão 4.6.7)

# Parâmetros da dinâmica de minimização

define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 200
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
nstenergy = 500
emtol = 10000.0
emstep = 0.01
cutoff-scheme = Verlet

# Parâmetros da dinâmica de restrição

define = -DPOSRES
constraints = all-bonds
integrator = md
nsteps = 50000
dt = 0.002
nstlist = 10
nstxout = 100
nstvout = 100
nstxtcout = 100
nstenergy = 100
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = v-rescale
tc-grps = protein non-protein
tau-t = 0.1 0.1
ref-t = 298 298
energygrps = Protein SOL
Pcoupl = Berendsen
refcoord_scaling = all
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 298.0
gen_seed = 116247
cutoff-scheme = Verlet

# Parâmetros da dinâmica principal

define = -DFLEXIBLE
constraints = all-bonds
integrator = md
nsteps = 500000
dt = 0.002
nstxout = 1000
nstvout = 1000
nstxtcout = 1000
nstenergy = 5000
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
Tcoupl = nose-hoover
tc-grps = protein non-protein
tau-t = 0.4 0.4
ref-t = 298 298
energygrps = Protein SOL
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 298.0
gen_seed = 116247
cutoff-scheme = Verlet