[gmx-users] water box moves during MD simulation

[Ming Tang]

Dear all,

After MD dynamic simulation for 100 ps, I found the water box was moving during the simulation, but my protein was inside the water box all the time.
Here is the . mdp file I used:

integrator       =  md
dt               =  0.001
nsteps           =  100000
nstxout          =  1000
nstvout          =  1000
nstlog           =  1000
nstxout-compressed        =  100
xtc-precision    =  10
cutoff-scheme    =verlet
rlist            =  1.4
coulombtype      = reaction-field-zero
coulomb-modifier = potential-shift-verlet
rcoulomb-switch  =  0.8
rcoulomb         =  1.4
epsilon_r        =  15
vdw-modifier     =  potential-switch
rvdw-switch      =  0.8
rvdw             =  1.4
tcoupl           =  v-rescale
tc-grps          =  Protein non-protein
tau-t            =  1.0 1.0
ref-t            =  300 300
Pcoupl           =  parrinello-rahman
Pcoupltype       =  isotropic
tau-p            =  12.0
compressibility  =  3e-4
ref-p            =  1.0
refcoord_scaling =  all
pbc              =  xyz
constraints              = h-bonds

Could anybody tell me what's wrong with my .mdp file?

Thanks in advance.