[gmx-users] problem while removing extra waters from a simulation box, simulation explodes thereafter

[maria goranovic]

Hi

I have run a lipid bilayer simulation, which has too much water in it and
too few lipids (small bilayer patch, ~ 80 waters per lipid). I have used
genconf to multiply the system in the xy direction to increase system size,
and then removed water which is z<8 angstroms and z>92 angstroms using vmd
to decrease my system size and remove unrequired water. After I run editconf
on the truncated system getting it to the right box size, the energy
minimization keeps exploding on me with lincs errors? I think this is
because my (0,0,0) does not coincide with one corner of the simulation box.
Or is is something else? In either case, how can this be fixed????

-- 
Maria G.
Technical University of Denmark
Copenhagen
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