VMD-L Mailing List

From: Arthur Oliveira Vale (arthurovale_at_uchicago.edu)
Date: Fri May 19 2017 - 18:52:11 CDT

Dear All,

I'm running a hexagonal membrane system and would like to set up the vectors for the periodic images so that they correctly match the sides. I've tried doing the following:

pbc set {123 0 0 60 90 90}

where 123 is the desired size for the vector. Despite that, vmd displays the periodic images as if the alpha angle was set to 90. I've tried changing the alpha angle directly with "molinfo top set alpha $alpha" where $alpha is some angle, and no matter what angle I choose for $alpha my images are the same. Would anyone know why "molinfo top set alpha x" is not working? Also, how can I set the periodic vectors for a hexagonal system?

Thank you in advance,

Arthur Vale