From: John Stone (
Date: Wed Aug 24 2011 - 12:43:52 CDT

If you know the initial orientation and the orientation
required to match your experimental information, you should
be able to compute 4x4 transformation matrices (composed
of of all necessary translations and rotations) for each of
the components of your model. Once you've computed the require
matrices, you can use the atomselect "move" subcommand to apply
the transformation to the initial structures for each component,
to obtain your final model. You have some geometry work ahead of
you, but please see the VMD User's Guide and various VMD tutorials
for examples.

  John Stone
On Wed, Aug 24, 2011 at 05:48:38PM +0100, Anna wrote:
> Dear vmd developers/users!
> I need to orientate cylinder-shaped polymers in order to simulate them
> with LAMMPS, and I was given data for their initial orientation and
> position from other experiments.
> I have the following information: the coordinate (r) centre and
> orientation vector (n) of long axis.
> chain one: r1_x; r1_y; r1_z; n1_x; n1_y; n1_z
> chain two: r2_x; r2_y; r2_z; n2_x; n2_y; n2_z
> chain 1: -0.8; -2.1; 0.5; -0.07; 0.8; 0.5
> chain 2: 2.6; 1.9; -2.2; -0.08; 0.9; 0.4
> I am confused as to how I can approach this problem using vmd.
> Thank you in advance for any input!

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