VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Nov 13 2006 - 15:37:46 CST

Are you using periodic boundary conditions? This can happen if something
gets transposed across a periodic boundary. In this case, you need to
unwrap your coordinates first.
Peter

Nels Thorsteinson wrote:
>
> I use "measure rmsd backbone $reference" to obtain rmsd curves.
>
> Once in a while, one of the frames rmsd values is up to 30 angstroms
> higher for a single frame than all the others -an obvious mistake/bug
>
> Sometimes doing align_frames twice before calculating the rmsd fixes
> the problem, and sometimes it does not.
>
> Can this be fixed? Is there a work around?
>
> Thanks, Nels
>