From: Grace Brannigan (
Date: Wed Nov 16 2016 - 09:11:51 CST

Jerome, I'll just add that your github page says it's 10-30 times faster
for your "own purposes".

With systems ~ 200,000 atoms, we see a speedup of at least that much.
Definitely appreciated!


Grace Brannigan, Ph.D.
Assistant Professor
Graduate Program Director, Center for Computational and Integrative Biology
Department of Physics
Rutgers University, Camden, NJ

On Wed, Nov 16, 2016 at 8:54 AM, Jérôme Hénin <> wrote:

> Hi everyone,
> This is a reminder that there is a faster alternative to pbc wrap from the
> PBCTools plugin, in the form of qwrap:
> It has improved since the last time I mentioned it on this list,
> specifically, you can now restrict the wrapping to a given selection, as in
> (my personal favorite):
> qwrap sel "not protein" center protein
> Thanks to a contribution by Giacomo Fiorin, wrapping can also be done
> based on VMD fragments.
> Qwrap is written in C and is relatively simple-minded, hence the speed.
> The main limitation with respect to pbc wrap is the treatment of
> orthorhombic cells only - however that can change in the future.
> As usual, feedback is welcome.
> Jerome