[gmx-users] uneven distribution of water across the bilayer

[Alok]

Dear All,

I am trying to simulate lipid-water system (340 POPE lipids & 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have observed a zone between the lipid head group and water. I tried to do small simulations (50 to250 ps) using different pressure coupling but still I am not getting the structure which have homogeneous arrangement of water over lipid head group. There is uneven distribution of water across the bilayer. During this sort simulations position restrain on lipid was applied.

I tried Isotropic, semiisotropic,anisotropic pressure coupling with the following parameter, but no luck 

Isotropic:
Pcoupl                       = Berendsen
Pcoupltype                = isotropic
tau_p                         =   2.0
compressibility         =  4.5e-5
ref_p                          = 1

semiisotropic: 
Pcoupl                       = Berendsen
Pcoupltype               = semiisotropic
tau_p                        =   2       2
compressibility        =  0       4.5e-5
ref_p                         =  0       1.0

anisotropic:
Pcoupl                      =  Berendsen
pcoupltype               =  anisotropic
tau_p                        =  10.0       10.0        10.0      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

I also tried NVT Ensemble but no success till now.  could some one give some idea what parameters I should take to overcome this problem. I searched the mailing list this problem discussed so many time suggestion was after sort simulation (10-20 ps) water will arrange properly,but I am not able to get proper arrangement of water molecules. please suggest me where I am doing mistake.


Other parameters od the MDP file.

define                     = -DPOSRES_LIPID 
integrator               = md
dt                            = 0.002
nsteps                   = 25000
nstcomm               =  1
nstxout                  = 1000
nstvout                  = 500
nstlog                   = 100
nstenergy              = 100
nstxtcout                = 500
xtc_precision        = 1000
xtc_grps               =  POPE  SOL
energygrps          =  POPE  SOL
nstlist                          = 10
ns_type                       = grid
pbc                             = xyz
rlist                             = 0.9
coulombtype              = PME
rcoulomb                   = 0.9
rvdw                             = 1.2
fourierspacing           =  0.12
pme_order                 =  6
ewald_rtol                  =  1e-5
optimize_fft                 =  yes
vdw-type                     = Cut-off
gen_vel                          = yes
gen_temp                     = 300
gen_seed                     = 173529
constraints                   =  all-bonds
constraint_algorithm    =  lincs
unconstrained_start     =  no
lincs_order                     =  4
lincs_iter                         =  1
lincs_warnangle           =  30



Thanks in advance,
Alok
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071019/77223275/attachment.html>