[gmx-users] peptide-membrane simulations

[maite lopez]

Hi:
I am working on peptide-membrane simulation under lipid (DPPC, from
Peter Tieleman group site). I've solvated the system using the x and y
vectors of the initial box (membrane box), but i increased the vector
in the z axes . I've
eliminated the water molecules that are interacting with the apolar coils of the
lipids, but when i try to reorder the atoms with the editconfig command it gives
this error :
Fatal error:
Invalid line in peptide_dppc64_water.gro for atom 20704:
   4.72500   4.23200  12.00000

this is a water atom. I eliminated this water molecule and the same
error comes. The line format is ok.

If i eliminated in the initial .gro only a water molecule that it is
interacting with
lipids the same happen.

i visualizated the system and these atoms aren't in contact.

I've done the last steps because when i run a MD of the unmodified system,
the water molecules that are interacting with the apolar coils of the
lipids form clusters between the monolayers.

How can i eliminate this molecules or solvate the system only in the z axes?

I want to add more water molecules and to equilibrated other membranes
of this site, but i'll always obtain water molecules between the
monolayers.

 Any help will be highly appreciated.

 Maite