VMD-L Mailing List

From: Grace Brannigan (grace.brannigan_at_rutgers.edu)
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

Grace Brannigan, Ph.D.
Assistant Professor
Graduate Program Director, Center for Computational and Integrative Biology
(CCIB)
Department of Physics
Rutgers University, Camden, NJ
branniganlab.org
BSB-426
(856)225-6780

On Wed, Nov 16, 2016 at 8:54 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> 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:
> https://github.com/jhenin/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
>