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

maria goranovic mariagoranovic at gmail.com
Tue Jun 22 15:43:25 CEST 2010


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
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