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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