Hi Gromacs users,
I think I am a bit confused about the proper way to handle boxes that
are not standard cubes. I'm trying to run a membrane simulation where
a cyclic undecapeptide is inserted into the membrane and I want the
water layer to be sufficiently thick that if it were pulled, the
peptide could be fully solvated by the water. To avoid having an
enormous box of membrane and water, I have an orthorhombic box
containing my peptide and bilayer. It minimizes alright with Gromacs,
but when I go to equilibrate it it fails because it's too skewed to be
a triclinic box. I've tried modifying the box with editconf and
converting it to a rhombic dodecahedron, sort of like the manual
suggests for a membrane system. I'm not sure that even that is
sensible since it seems like I would be losing content that way, yet
nothing is clipped, and I did this after using trjconv to remove any
periodicity from my prior simulation of this system (in Desmond) but
doing so gives me a starting potential energy of NaN for the new
system that I obviously cannot work around. Is what I am trying to do
even possible? If it is, it seems like there is probably a better way
than the way I chose, so if you have any suggestions, I would be
greatly appreciative.
I'm trying to run this simulation with AMBER FF99SB parameters for the
peptide, Tieleman's lipid parameters for POPC, and SPCE waters, so
just as a sanity check, is it reasonable to consider a system like that?
Thank you,
Katrina
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