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
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