  We present a new cosmological zoom-in simulation, where the zoom region
consists of two halos with virial mass M_v~5x10^{12}M_{sun} and a ~Mpc long
cosmic filament connecting them at z~2. Using this simulation, we study the
evolution of the intergalactic medium in between these two halos at
unprecedented resolution. At 5>z>3, the two halos are found to lie in a large
intergalactic sheet, or "pancake", consisting of multiple co-planar dense
filaments along which nearly all halos with M_v>10^9M_{sun} are located. This
sheet collapses at z~5 from the merger of two smaller sheets. The strong shock
generated by this merger leads to thermal instabilities in the post-shock
region, and to a shattering of the sheet resulting in <~kpc scale clouds with
temperatures of T>~2x10^4K and densities of n>~10^{-3}cm^{-3}, which are
pressure confined in a hot medium with T~10^6K and n>~10^{-5}cm^{-3}. When the
sheet is viewed face on, these cold clouds have neutral hydrogen column
densities of N_{HI}>10^{17.2}cm^{-2}, making them detectable as Lyman limit
systems, though they lie well outside the virial radius of any halo and even
well outside the dense filaments. Their chemical composition is pristine,
having zero metalicity, similar to several recently observed systems. Since
these systems form far from any galaxies, these results are robust to galaxy
formation physics, resulting purely from the collapse of large scale structure
and radiative cooling, provided sufficient spatial resolution is available.
