On 6/04/2012 3:36 PM, Albert wrote:
hello:
thank you very much for your kind messages. I first did
minimization, the NVP with gradually heating the system from 0-310K,
and them NPT production:
----NVT.mpd---------------
define = -DPOSRES -DPOSRES_LIG
constraints = hbonds
integrator = md
dt = 0.001 ; ps !
nsteps = 3000000 ; total 3000.0 ps.
nstcomm = 10
nstxout = 5000 ; collect data every 1.0 ps
nstxtcout = 5000
nstvout = 5000
nstfout = 0
nstlog = 10
nstenergy = 50
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.4
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 310 310
; Pressure coupling is off
Pcoupl = no
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
pbc = xyz
annealing = single single
annealing_npoints = 2 2
annealing_time = 0 5000 0 5000
annealing_temp = 0 310 0 310
gen_vel = no
constraint_algorithm = Lincs
---NPT md.mdp--------------------------
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
This time step is normally too long for those constraints. See manual 6.5.
nsteps = 5000000 ; total 10ns.
nstcomm = 10
nstxout = 20000 ; collect data every
nstenergy = 20000
nstxtcout = 20000
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
vdwtype = cut-off
rvdw = 1.4
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
DispCorr = no
; Berendsen temperature coupling is on
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 310 310
; Pressure coupling is on
Pcoupl = parrinello-rahman
Don't use algorithms that are known to be unstable for equilibration
while you are doing equilibration. See manual.
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 310 K.
gen_vel = yes
Why bother doing slow heating if you're just going to re-initialize with
random velocities again?
Mark
gen_temp = 310.0
gen_seed = 6666
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