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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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