[gmx-users] Box size/type confusion for bilayer system

klexa klexa at umich.edu
Thu Oct 18 20:43:34 CEST 2012

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,


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