[gmx-users] peoblem with water

[sudheer babu]

Hi all,
I embedded protein into membrane. After that *EM and *PR running fine but in
position restrian intial step, one side of the membrane layer, water
molecules move to second side although total structure looks cubic form,
Only problem with diplacemnt of water to otehrside. Shall I run it for
longer time? I may get equal number of water molecules both sides.

I am pasting my pr.mdp file (Fc on protein 1000)

title               =  dpt pos restrained
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  10000    ; total 50 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.4
pbc                 =  xyz
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein   POPC   SOL_Cl
tau_t               =  0.1       0.1            0.1
ref_t               =  310       310           310
; isotropic pressure coupling is now on
Pcoupl              =  parrinello-rahman
pcoupltype          =  anisotropic
tau_p               =     1.0    1.0    1.0    0    0   0
compressibility    =  4.5e-5   4.5e-5  4.5e-5   0   0   0
ref_p               =    1.0    1.0   1.0     0    0     0
; Energy monitoring
energygrps          =  Protein   POPC   Sol_Cl
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  310
gen_seed            =  173529

Pls help me
Thanks in advance
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