[gmx-users] Periodic Boundary Condition Issues

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 22 17:27:44 CEST 2009

Cooper, David R wrote:
> Hello,
> 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?

The trjconv -pbc options were designed to fix this sort of issue.  Dimers and 
complexes can be a bit tricky, so you'll have to play around with different 
options to find the one that works for you.


> Thanks,
> David
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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