VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Nov 18 2016 - 18:46:56 CST

Hi Norman and everyone,

A quick unwrapping feature is now available as "qunwrap".
https://github.com/jhenin/qwrap

Please give it a spin and let me know what you think!

Jerome

On 17 November 2016 at 10:09, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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
>>
>
>