VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 20 2013 - 16:03:08 CST
I would think you'd get the same principal axis if there is no
difference other than translation of identical structure to a new
origin, but without more information it's hard to say what may
have gone wrong in your specific case.
On Sat, Dec 21, 2013 at 01:39:28AM +0530, ssaurabh_at_physics.iisc.ernet.in wrote:
> Hi all,
> 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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-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/