[gmx-users] Re: job failed

[Albert]

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 !
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
Pcoupltype    = isotropic
tau_p        = 1.0
compressibility    = 4.5e-5
ref_p        = 1.0
; Generate velocites is on at 310 K.
gen_vel        = yes
gen_temp    = 310.0
gen_seed    = 6666

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