[gmx-users] problem in pr.mdp file

[sudheer]

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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