[gmx-users] Periodic Boundary Condition Issues

Cooper, David R cooperdr at rose-hulman.edu
Wed Jul 22 17:12:43 CEST 2009

I am trying to analyze the trajectory of the estrogen receptor alpha in water.  As you know, the ER is a dimer and as such when it approaches the boundary for the simulation one of the monomers jumps to the other side of my box and thus screws up any post simulation calculations that we are interested in, especially since the focus of our project is the dimerization interface.  Is there any way to fix this so that visually the dimer doesn't appear to split?

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