[gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?

[Mark Abraham]

Alok wrote:
> Dear Chris,
> 
> Thanks for your time and suggestion.
> I tried all the possible pressure couplings (including semiisotropic) 
> and run it for around 500ps.Gap between head group and water molecule 
> disappear, but I was getting uneven distribution of water molecules. I 
> am pasting my previous mail again. Hope I will get any solution for my 
> problem.
> 
> 
> Best Regards,
> Alok
> 
> 
> ##############################################################
> 
> Dear Mark,
> 
> Thanks a lot for your valuable time, and sorry for inappropriate
> description, I am describing again, I hope thin time I can make it clear.
> 
> I took preequilibrated POPE.pdb files which already have SPC water 
> molecules
> I had deleted these water molecules

Why not leave them?

> and change the box size at 'Z Axis'
> only, so I can accommodate more water, then using genbox I had added TIP4P
> water molecules, but it also added the water molecules in the interior of
> the bilayer. So I deleted these water by the criteria if the 'Z' coordinate
> of the water in between the 'Z_min' and 'Z_max' of 'C13' (where 
> branching of
> the POPE molecules start) atom. After that I got the files which don't have
> any water at the interior of the bilayer but there is a vaccuum between
> lipid head group and TIP4P water molecules (I defined it as a ZONE in my
> previous mail). 

The Z-coordinate-based water-removal procedure you describe can't create 
such a vacuum, so I can't follow your description.

> As discussed in the mailing list so many times I can do 
> same
> thing by increasing the VdW radius of lipid atoms. But after that I was
> expecting these vacuum will be vanished and water molecules will spread
> homogenously after sort span of MD, as suggested in the mailing list. But
> here problem has started I run MD till 500ps, but water molecules are
> clustered at some places, at some places there is no water or very less
> water. i.e. I am getting uneven distribution of water molecules over lipid
> head groups.

I'm afraid I can't understand what you mean by "uneven distribution" in 
the absence of a picture or a structure.

> So I thought this problem might be due to pressure coupling or type of
> ensemble I am using (might be I am wrong here !).
> 
> I ran four different sort MD by using isotropic, semiisotropic, anisotropic
> pressure coupling and last one no pressure coupling (NVT ensemble). But in
> all the cases I am getting similar structure at last which is uneven
> distribution of TIP4P water molecules over head groups.

I made suggestions about your parameters last time. You don't seem to 
have followed them.

Mark