[gmx-users] problem regarding protein in water simulation

[sudheer babu]

Hi all,
my protein contain 59 aminoacid residues and crstal water molecules  103,
 The steps i have done are
1.minimisation of protein invacuo
2.added simulation box of 6 in xyz dimensions
3.added water
4.added ions
5.energy minimisation in water
6.positoin restrain in water
7.production step......
My sytem is fine till 250 ps production , after that protein is coming to
outside from water box,
 whats the problem ?
have i done any mistake while doing steps or any mistake in md.mdp file
pls help me...
along with my mail, md.mdp file is attaching here,
*md.mdp*
title                   =  dpt_prod
constraints          =  hbonds
integrator           =  md
dt                    =  0.002    ; ps !
nsteps              =  125000   ; total 250 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.4
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein   Sol  CL-
tau_t               =  0.1       0.1  0.1
ref_t               =  300       300  300
; isotropic pressure coupling is now on
Pcoupl              =  Berendsen
pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Energy monitoring
energygrps          =  Protein  Sol  CL-
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300
gen_seed            =  173529
                                                             39,1
Bot
Thanks in advance.
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