Thanks for response Mr.Alan Dodd
1) 1st run is simularion of position restrain of protein in water (25000 steps)
- system running very very slow means for completion 10 steps it is taking
more than 5 minutes or more
2) 2nd simulation is production step of popc in water (125000 steps ) - this is
going normally means for completion 10 steps it is taking 3seconds or less than
that.
i will send you the both input files of pr.mdp and md.mdp files
pr.mdp file ( This is already sent)
title = Yo
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 25000
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
; Berendsen temperature coupling is on in two groups
; Pressure coupling is on
Tcoupl = berendsen
tc-grps = Protein SOL Na+
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
Pcoupl = parrinello-rahman
pcoupltype = isotropic
ref_p = 1
tau_p = 0.5
compressibility = 4.5e-5
; Energy monitoring
energygrps = Protein SOL Na+
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
md.mdp file
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 125000 ; total 250 ps.
nstcomm = 1
nstxout = 50
nstvout = 10
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = POPC SOL
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = POPC SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
pls anyone help me
thanks in advance......._______________________________________________
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