[gmx-users] POPC simulation

[Moutusi Manna]

Hi
  I want to perform   peptide + popc membrane simulation. I download popc128a.pdb from
  (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
  Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of the peptide .I increase the water layer using the following commands
  1. editconf  -f  popc128a.pdb  -o  po_box.pdb  -box  6.1065  6.1059  9.0000  -c
  2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top
   
  Now, the no. of water molecules over the bilayer  increased . But, the problem is that  there are water molecules inside the bilayer, which were absent incase of popc128a.pdb. How can I remove these offending water molecules?

       
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