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

[Mark Abraham]

Alok wrote:
> 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. 

You'll have to describe that "zone" better if you want us to understand 
what you're talking about. Read genbox -h where it mentions vdwradii.dat

> 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. 

Are these last two observations related, or not?

> During this sort simulations position restrain on lipid was 
> applied.

Check your waters aren't restrained too.

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

I think you need to read section 7.3.14 of the manual. You're using 
combinations of parameter values that don't make sense.

> 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. 

So the problem is something other than the way you're setting up your 
ensemble.

>  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

That looks OK at a glance.

Mark