VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Sep 07 2006 - 17:53:22 CDT

Hi,
I have a simulation of pepitde-solvent system. During my analysis, I am
positioning the 4 atoms at each peptide bond in a certain manner at the
origin and in the X-Y plane.
Due to the operations, and my system is not centered the origin anymore, and
the simulation box get rotated too. So, the minimum image convention is no
longer as straightforward as:
x_ij = x_ij - boxL*NINT(x_ij/boxL)

Can somebody tell me how to implement the minimum image convention in these
general cases, where the simulation box is shifted and rotated?

With thanks,
Neela