VMD-L Mailing List
Date: Fri Dec 20 2013 - 14:09:28 CST
I have prepared a system with two identical molecules placed with
exactly the same orientation at some distance . When I calculate the
principal axis vectors using Orient, I see that the the corresponding
principal axis vectors of the two molecules are not parallel to each
other (principal axis 1 of molecule 1 is not parallel to principal axis
1 of molecule 2 and so on). Shouldn't they be parallel, if the
molecules are exactly the same and have the same orientation? If not,
then why?? Kindly guide me on this.
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