VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Nov 17 2016 - 03:09:14 CST

Hi Norman,

You are not the only one to request such a feature. I'm definitely going to
implement that, but not as "remove long bonds", which is cumbersome and is
done by "pbc join" in PBCTools, but rather what I implemented in "pbc
unwrap", that is, remove large jumps from one frame to the next. That
requires a more or less continuous trajectory starting from a "clean"
configuration where all the fragments are in one piece.

Jerome

On 17 November 2016 at 09:05, Norman Geist <norman.geist_at_uni-greifswald.de>
wrote:

> Hey,
>
>
>
> thanks for your work so far. Would it be difficult to also implement a
> unwrap function (more or less remove long bonds)? Since f.i. GROMACS
> outputs trajectories always wrapped.
>
>
>
> Norman
>
>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Jérôme Hénin
> *Gesendet:* Mittwoch, 16. November 2016 14:55
> *An:* VMD Mailing List <vmd-l_at_ks.uiuc.edu>
> *Betreff:* vmd-l: Fast PBC wrapping in VMD
>
>
>
> 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
>