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

[Alok]

Hello Maria,

You can do it by two different methods.

1) You can increase the default VdW radii of the lipid atoms in  /usr/local/gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) )

2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline.

Hope it will help

Alok
  ----- Original Message ----- 
  From: maria goranovic 
  To: gmx-users at gromacs.org 
  Sent: Sunday, October 21, 2007 3:57 PM
  Subject: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?


  Hi

  I am using editconf to try to add water layers on either side of my bilayer. I use the following command:

  genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top

  However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer.


  - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ?

  Thank you

  -Maria



  -- 
  Maria G.
  Technical University of Denmark
  Copenhagen 


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